I just went through something similar to your problem. The right way to fix it is to replace those bolts with rivets. Trust me installing a rivet is just as easy as installing a bolt. I was leary at first too, but with the help and encouragement from the great folks on this site I got it done. The rivets I got from grainger at a little over $10.00 for a hundred. The originals were 5/32 but some were wallerd out so I drilled them all to 1/4 in. No sealant needed, just have a friend hold a piece of metal on the head side while you tap the other till it expands and tightens up. Just remove one bolt at a time and replace with a rivet, that simple. Very easy, you'll be surprised.
Me and a friend replaced every rivet in the entire boat in under 2 hrs. Then paint the steel flex on and you'll never have to worry about leaks,corrosion, or structural integrity.
once you put the steel flex on and those bolts rust out further a repair then is going to be a pain.Hate to see you do all this work and then have to do it again in a couple of years.