Rubber worm rattles used in bass fishing have a slim profile and can be placed several ways. Like GoNavy said just epoxy or goop the hole and your set. I've been trying to make one sound like a Smack-it cause they like them!
I use soft foam bodies for my poppers. You don't need a really large hole. I usually use a large needle to make the initial hole. I use the smallest glass rattles, available fairly cheap in the Bass Pro catalog, they do come in larger sizes but the small ones add little weight to the fly. I'll use either 5 minute epoxy or Zap-A-Gap to hold it in place or you can even push it in so it's completely inside the fly.
Can also insert the glass worm rattles into crease flies, balsa wood bodies, etc. Also, try using them them in non-popper, streamer type flies...eg: deceiver and clouser flies...tie to hook shank and wrap with flash. Very effective.