When I put my centreplate back in I'll just put a big fat 'O' ring behind a washer behind the nut on each end of the pivot, and pinch it up just enough to compress the rubber. I suppose you could cut a washer from some neoprene or similar as an alternative. I don't think that sealant as such would really work.
In one book I saw a suggestion for a hollow wooden cap to be bedded down over the nut/bolt head as a way of stopping leaks, but I prefer to have everything visible.
What sort of boat is it?
bead of sikaflex, hand tighten then leave to cure for a couple of hours before tightening fully. the sika will have cured enough so when fully tightened will go into compression like an o-ring, but will have some adhesive sika magic as well