Be very careful - the set JB weld is likely harder than the aluminum, even if it was poorly done. Any mechanical method you try - scraping, sanding, grinding is going to be harsh on the aluminum if you miss the JB weld.
I had an old 12' row boat where the leaks were really bad so I wasn't worried about burning out any puddy material between the riveted pieces of aluminum, so I took a torch to the aluminum to remove JB weld that was slopped on over time by previous owners...it was a bit of a beater boat so cosmetics weren't an issue. I applied an aluminum solder over the leaking rivets which worked well but was a pain in the *** to get the aluminum hot enough and warped the aluminum if you weren't careful (learned the hard way not to heat up anything but riveted rib sections). Probably would have worked better on a thick-skinned Alumacraft than the Sea Nymph I was working with.
JB Weld is an epoxy product, so expect similar issues with other products - though it sounds like the proper prep-work wasn't done for the JB application. At the end of the day actually welding or replacing the rivets is the only way to go if you want a quality end result.
If the rivets are all beneath the flooring you can try a "closed end blind rivet" https://www.rivetsonline.com/rivets-en/blind-rivets-en/closed-end-blind-rivets.html and put a small dab of silicone caulk in between each connection for added security. If you go this route you're best bet will be to drill out the entire rib, caulk each hole, then rivet back in place. On the plus side these are "pop-rivets" which can be done by one person working from one side of the boat, downside is the protruding rivet backside into the boat compartment - but as I said, if you've decked everything you won't see anything on the inside of the boat so it's a non-issue.