here's my stance: having certain diseases/common outbreaks doesn't necessarily mean the water quality is bad, but it should always be something that is looked at. Maybe the quality isn't so much 'bad' in general, rather some parameter IS off, particularly for given species.
example, german blue rams are not tolerant of nitrates, nitrites, or pH swings, and they do not do well in hard water IMO
. my planted tank water is just not suitable to them.
as for getting internal parasites, to me this is more an issue with quarantining processes, and the stock of fish that your LFS
is getting in.