They really are dirty in some locations, others have tanks that are taken decent care of.
The store here in Birch Run, has a weekly change up, decent selection and about 8 tanks that just seem cleaner than the other 12.
Less disease there than walmart, and other petsmart petco type store.
Honestly I've heard of people just dipping in hydrogen peroxide, or really weak vinegar or bleach even. On plants.
I believe that Quarantine is a very good option, having a small tank setup just to put things into to allow any disease or parasites to die off before putting into any tanks with any other inhabitants.