Critical stuff you definitely double bag. But stuff like extra layers or even a sleeping mat are things that can get wet but probably shouldn't and adding the extra bulk of waterproofing them just isn't worth it (to me).

True waterproofing generally isn't worth it. But not having to worry about a light-moderate rain or getting too close to a river/waterfall (obviously not submerged ,but just getting sprayed) is very nice. For the heavier stuff, you should probably throw a tarp/poncho/whatever over even the waterproof bags anyway.

Although my personal feeling is that if I am caught out in a heavy enough rain that just wearing my softshell and relying on zippers isn't sufficient then I don't want to be hiking anyway and should be looking for shelter.