I don't have a popup, but isn't the canopy vinyl?
Even if it's nylon, I'm not sure that bugbomb would interfere with scotchguard...I think that's a silicone base.
I wouldn't think a bomb would hurt anything - most of it's gaseous, and insecticidal residues will settle on inside surfaces.
I've used it in my trailer lots of times- haven't noticed any staining of fabrics or anything like that.
Just lots of dead bugs!
One more thing, now that I think about it-
Back in my tentcamping days, I used to set a bug bomb off in my canvas tent before I put it away for the winter.
I never noticed any damage from that, but it was canvas, not nylon...
Maybe other popup owners will chime in to advise something else, though.