I don't know anything about canopies or mounting them or anything like that. I do know, though, that you can go to your local hobby shop and get this stuff called Formula 560. For the most part, it doesn't attack or fog plastics. It's designed to glue canopies onto model airplanes.
You could try a bit of that on some scrap plexi to see if it attacks/fogs that, and then try a bit with a screw and nutplate and see if it works OK as thread lock. I would guess that it gums stuff up enough that it'd probably be OK and won't be too terribly hard to remove in case you have to. The important part is to TRY IT before you do it for real because I could be raving lunatic with nothing better to do than try to ruin people's airplanes
the manufacturer is
Pacer Technologies. They're arguably about the best in the business for consumer cyanoacrylates (i.e. crazy glues) as well as other types of glues and things.