I think this is an important topic and a really good question!
Personally, I believe that every LFS will have a pest of some sort due to probability. Even a small LFS rotates WAY more frags through their store than any hobbyist will through their tank. So its safe to say the probability of pests goes way up. Plus, the shear amount of time and work that would be put into quarantining the amount of coral a LFS would sell wouldn't make sense. Plus many stores take trade-in's from local hobbyists which are bound to have a few pests.
On a coral farm level, I believe its a different story. Take Tidal Gardens for example. The do receive new corals, but all new corals are separated and go through a strict quarantine procedure before being released into their grow out systems. It makes sense on this scale though because its a long term investment and generally they receive colonies and not just a small frag. So in turn they create and sell frags from colonies that are already quarantined. The amount of space and initial investment this requires is too great for most LFS.
Personally, I consider aptasia to be a pest along the lines of algae. It's not impossible to get rid of if I happen to get some in my tank. I've fought it before and it was an easy battle for me. So if I see a LFS with aptasia, I'm not particularly bothered. I think the overall cleanliness of the tanks, health of the corals and fish, speak what I need to know about the store I'm in. My favorite LFS has aptasia growing in the corners of every tank but every coral is healthy and spotless. Every tank is algae free, all fish are fat and disease free. In fact, out of all the LFS's I've every been to, I'd be hard pressed to find a cleaner tank. I've been in plenty of stores that I wouldn't touch the water let alone buy anything from their tanks even if I don't see aptasia.
In short, I think it all comes down to judgement. If you really want corals you can assume are pest free, find a trusted coral farm like WWC or Tidal Gardens who quarantine all new corals, and only sell frags from their colonies. Even then, people will tell you to still watch for pests. I really think it all comes down to how much risk you're willing to take on, which everyone is going to have a different answer for.