As a store owner this is a great question... As a general rule it is always advised, if you can, to QT your fish. Just to give yourself the best chance at a successful reef tank. No Quarantine is 100%. But the more precautions you take, generally the better off you will be.
There are precautions that we take that have greatly reduced fish loss and provided us great results. We have 50 years in the business so we have tried many things. If your store is getting transshipped fish then a quarantine is quite possibly the best option at the store. That is one of the reasons we order from a wholesaler that does the transship and quarantine for us.
1) What we do on fish arrival is acclimate the fish. (you should follow this properly at home as well). We have tried drip acclimation and just letting the fish sit in the bags in the aquarium for 20-30 minutes. With our in-house testing we find that our fish loss is the same with just letting the temperature regulate serves just as good as drip acclimation. Now that is not discounting drip acclimation, as that is a perfectly acceptable method as well. We attribute this to our fish vendors water chemistry and ours being close to the same. The further apart the chemistry is the slower you need to acclimate.
2) We then start our fish on a medicated food diet for at least the first 7 days. We use a combo Seachem Metroplex, Focus and Garlic Guard added to thawed frozen spirulina and mysis. This is a low dose (food treatment vs treating tank) so it is easier on the fish during this phase. Its low enough dose that we go ahead and feed all of our fish this medicated food. Now we do not feed this to puffers, eels, & seahorses, etc as they are sensitive to medications.
3) Most LFS will have some food on hand to feed the fish. Ask them to feed the fish so you can see them eat. At our store we turn our fish tags sideways on new fish so we/customer know if the fish have eaten yet. Once they eat we turn the tag back horizontal to let everyone know they are eating now. Don't buy fish with sunken stomachs. This means they have not eaten and are possibly on the decline.
In our store we try to give you every effort to get fish that are as healthy as possible. Even without getting fish wholesaler that has QT their fish we still accept a great deal of fish loss so that you do not have to. That being said giving your fish another week or two in a quarantine tank will give them time to adjust to your tank parameters and give you time to observe any thing going on with your new fish.
