Check the size and thread count of the good nuts and get some replacement nuts that are identical to the originals. When the boat is hauled and resting on the keel, carefully slit one of the worst nuts (you can do this with patience and a dremel with slitting discs) and used a chisel and 2 pound hammer to split the nut. DO NOT SLIT THE NUT SO FAR AS TO DAMAGE THE THREADS ON THE BOLT. It will split without goint that far.
It is possible that the threads on the bolt that were covered by the nut are fine. Remove most of the top of the bolt, leaving only enough to rise 1/4" above the new nut. Clean up everything else, including the threads at the top of the bolt, and carefully install the new nut, torquing to factory specs. Do the same to the other bad nuts.
Then, make a decision to have the yard strengthen the hull/keel joint by adding several more bolts.
One of the real problems with these keel bolts isn't the corrosion in the bilge, which is a problem, but the corrosive 'necking down' of the bolts directly in the joint between the keel and the fiberglass. For some reason, I have found far too many of these keel bolts withered to less than half their original diameter.
If torquing the original bolt you fix doesn't snap it off, then you might assume yours are OK. If it does, then you know you must have the yard do the "fix" you described.
Don't feel bad if you have to do it - once it's fixed, it will be fine.