I've seen anchor worm, cotton mouth, dropsy, fish lice, ich and various fungal infections at different times in different stores. Yeah fin rot & SBD too.
I know there is a certain amount of dead/dying fish at the lps - but I like to see that they remove them regularly & not leave them to be eatern/infect other fish
I usually ask if they have a central filtration unit or if the tanks are each on their own (or which ones share) if I see something in one tank that looks nasty.
In my local pet stores it is usually the worst after a new shipment. There are a couple of suppliers that really are terrible & I know those fish will be sick. Also I see more ich when the weather is changing (like winter to spring).
I've bought fish with ich (not terrible cases) (as I have been pretty successful treating it & I have a QT tank) but I pretty much draw the line at anything else.
I agree with Laurie - watch the fish carefully.