I usually remove the MAQS after the treatment ends, more to make sure everything is alright. It can cause queen loss, but I haven't seen that yet. Last year we had a hot spell and I did cook one hive, lots of dead bees and frames of dead brood.
Lazy shooter, to answer your question, if you only have a few hives it is possible to do mite counts and determine whether you need to treat or not. When you have hundreds of hives it is not so easy. Treating the hives that need it and not treating those that don't would be a time and costly endeavor. Most commercial keeps would do sample testing in yards and if mite counts are high the entire yard gets treated, which makes sense in my opinion, simply because the odds they are all effected is great.
Formic is also effective against tracheal mites, although they no longer seem to be the problem they once were.