Depending on the severity and location of the leaks, you may be able to simply tighten the through bolts. I had a similar problem is a very localized area and that fixed the problem. One bolt was stripped; I suspect that the PO had tried to fix the problem by over tightening. I rethreaded the bolt and it's been fine ever since. You are correct that silicone won't fix the problem.
There is no way that I would ever break a hull to deck joint in an effort to fix it. I'd either a) live with the problem or b) walk away. Just my $0.02......
Sabre 38 "Victoria"