Amanda, see below for some answers to your questions.
1. Do you think that I should use copper in the hospital tank or do the hypo salinity method?
The balance here is looking at what you're treating for, and what stress factor the medication itself has. Various types of copper are often used for external parasites, but they do little for the potential bacterial infections from the injuries from the parasites. There's even great debate amongst the preference of one type of copper over another. The overall idea with most medications is that we're putting the fish and parasite through something that the fish can survive and recover, but that the parasite cannot. Sometimes a 'quarantine' tank is more of an 'observation' or 'acclimation' tank. During which the fish is observed for signs of stress, given plenty of opportunities to feed on a variety of foods, etc. Once the fish is eating aggressively and shows no signs of disease etc, some folks consider that a successful quarantine perhaps in as short of time as a few days of a week. Depending on the pest you're focusing on however, as mentioned in the life cycle of ich mentioned previously, a full quarantine for ich could be as long as 6 weeks. Just with our own health, a holistic approach is often used that focuses on prevention, treatment, immunity etc. Hyposalinity is an option as well as many other ich treatments, however the bulk of my experience is from using some or all of the following dips, copper, UV, good water chemistry and quality food soaked in garlic (although we also soak our foods in lipid and vitamin supplements as well) One thing you'll find as I'm sure you've seen some already is that the aquarium hobby is full of a diversity of opinions and it can be an interesting sea to navigate to know what actions to take yourself. I find some of the same struggle each year with my journey with organic vegetable gardening with all the different opinions for preparing the soil, controlling pests etc.
2. Moving forward do you recommend I quarantine everything I buy including snails, corals, shrimp or just fish?
Surely quarantine is one of the most if not the most valuable tool to prevent and treat disease. Sadly most aquarists do not quarantine anything and everything simply goes right into the tank. With the decision to quarantine something you'll want to consider a couple things. First, what would a functional quarantine tank for the organism look like? Second, what problems/pests could the organism be bringing in? For example a quarantine tank for corals would need adequate lighting, water flow etc. A quarantine tank for external parasites on fish using hyposalinity or copper would be lethal to the coral, so there's not an overlap there. Another consideration is utilizing something that might be better referred to as a 'observation' or 'acclimation' tank. This would be a smaller version of the main display, where some new acquisitions go and are observed and allowed to recover from the stresses of shipping etc before going into the main display. The more diverse the inhabitants in the "quarantine/observation/acclimation" tank though the more limited the treatment options are, so this is important to consider. Once concern more and more with many corals being aquacultured is that often the parasites that prey upon these corals are being cultivated as well. While some parasites such as acropora red bugs can be eradicated fairly easily, others that lay eggs that are resistant to the treatments can be much more difficult to eradicate such as montipora or zoanthid eating nudibranchs. There's a lot of information there, but in a nutshell, the most needed items to consider quarantining would be fish and corals. The likelihood of 'importing a problem' with snails, crabs or shrimp would be very unlikely.
Finally, consider the background of a fish/coral etc before you get it. Was it shipped overnight and bagged up for 24+ hours, or for just an 1.5 drive home from the LFS? Was it eating when purchased? How long since it was shipped previously? Many stores simply offer fish up for sale the day they arrive. In this situation the fish hasn't recovered from that shipping stress and is about to endure another. Surely not a strategy doomed to failure, but also a stress unwise to ignore.
3. How long should the quarantine period be for each to keep the possibility of Ich out of my tank.
It depends on the type of treatment being used, but a full and complete quarantine ich specifically could be as long as six weeks as your waiting for all of the trophonts to hatch, then fail to find the host fish. With warmer temps this can be shortened to 2 weeks or so, but the tolerance of the specific fish to the higher temp should be considered. For some freshwater fish treatments such as with cardinal tetras, we'll keep the temps at 86 for the first couple weeks they are at the store for an example.
4. So now I can almost quarantee that Ich is in every single tank at the LFS and I have seen fish put in with the coral frags they sell as well. Is ich in every tank in a LFS normal and it is just something we have to quarantine out?
This gets back to that core argument of whether a tiny bit of ich is present in most systems with any fish population. If you're on the theory on maintaining a tank completely devoid of ich, then theoretically yes you would quarantine anything that came out of any tank that had a fish in it anytime in the last 6 weeks or had anything put in it within that last 6 weeks that came from a tank that had a fish in it in the last 6 weeks as one of those trophonts could be stuck to the base of that coral, on some live rock, on some sand, on the shell of a snail, etc and then move to your tank hatching up to 6 weeks later and releasing the tomites etc. Hence part of our argument that a little bit of ich is in almost every saltwater tank everywhere that has any fish in it or has had anything added to it from another tank that has had any fish in it. At the same time, ich is very seldom lethal, and in our experience, a fish that is eating aggressively whose only symptom is a couple spots will quickly recover and show no further symptoms. Now if the fish is all cloudy eyed, respiring heavily etc, that's a different story. The practicality of the above approach seems questionable though IMO.
Having treated these mild symptoms of ich (the few spots) many of times successfully in reef aquariums with corals/inverts etc, our approach is focusing on promoting a healthy immune system through quality food, and the use of UV on the main display. With this approach we generally see tanks with little to no fish loss, and little to no visible symptoms of disease running for years on end. Having the fish in under 'quarantine' or 'observation' before putting them in the main display makes success even easier.
5. I did not like the recommendation to just put up with ich because it is in every tank, isnt the idea to keep the parasite Ich out of your tank altogether and not have it contanty trying to find a slightly less immune fish?
I don't like the idea either, nor the idea that there's germs and other harmful organisms that I'll encounter today as I go to the grocery store, grab a shopping cart that others put their hands on, flush a toilet handle, etc. The practices however of these items being cleaned periodically, and my washing my hands helps keep me relatively safe. That's the same perspective we take on many fish diseases. It's not that they get ignored, in fact we focus heavily on it with 3 full time staff members whose primary responsibility is ascertaining the health of our fish, and implementing treatments. At the LFS level, we focus on buying fish from the best suppliers, hand picking when possible, and isolating, observing and treating our fish upon arrival to get them as healthy as possible before leaving the store to go to your aquarium. Next time you're in, feel free to have us show you some of the information we can share about the background of the fish. For example, we can let you know the date the fish arrived at the store, feed them for you so you see them eating etc. We're happy to do all of the above to ensure that you take home only the healthiest fish. At the hobbyist level, the focus could include and additional quarantine or observation period at home, treatment/prevention in the tank itself etc. The combination of the two sets up a ripe environment for long term success with fish health.
Here's also a link to something I wrote, geez, 4 years ago, I'm getting old...
that describes how we handle fish. I'm going to consider adding an addendum to it that guides to the benefits of home quarantine as well, and some examples of how to set up simple and relatively inexpensive quarantine tanks for corals, fish etc.