I recently purchased an Ortlieb handlebar bag. It bothers the crap out of me. The snaps rattle. I put some rubber (shelf covering) between the plastic form and the vinyl(?) waterproof outside layer, but... the snaps rattle. Will I damage the snaps if I put caulk, rubber cement or even some JD Weld (leftover from my Pepsi can stove) between the moving parts of the snaps? Has anyone else had this problem?

Is the outer decorative cover and the snap itself rattling? Is there enough space between the two to wrap some plumber's teflon tape?

you are talking about the two snaps for the Map case? Inside the snap is tiny metal ring that tensions the snap, that is what is rattling. I assume you are not useing the map case because mine will only rattle when there is no map case attached. If you are never going to use a map case you can dab some latex caulk or silicone in there.
If you want to be able to use the Mapcase at some point . take the bag with you to a hardware store or Fabric/craft store and get the male button that fits the snap on your bag.

I have the map case, but have not toured with the handlebar bag and panniers yet so I don't want the map case flopping around. Good idea about the male buttons. Now, I've got to get the "Incredibile Bell" taken off, it rings with every bump. The other day, a person I was riding with commented on how "loud" my bike was and how it made the bumps seem worse. Thanks for your help, I tried googling fasteners, snaps, etc. to no avail.

https://www.kingrichardco.com/snaps/Default.htm

This is one of the reasons I returned my Ortlieb. It rattled like crazy. I went with an Arkel and never looked back. The Arkel has alloy bar mounts not requiring "Marlin spike seamanship" or the cable that is integral to Ortlieb. Too many other plus featues on the Arkel to mention.

Richard