Many of the yukkiest, most pointless, timewasting activities in boat building and repair are all down to the misuse of silicon sealants. Generally if there is a leak some handyman type will try and fix it with this awful stuff. It is absolutely fine in bathrooms and houses but it just does not belong on boats. Why?
silicone sealant - no, no, no.
You can't paint it.
You can't sand it.
It doesn't stick well enough to be structural or to stop boat type leaks in its own right
It doesn't stick poorly enough to be easily removed.
When the thinners from paints hit it they spread its unpaintability to nearby areas which it hasn't contacted directly. YOu can the wash and sand to try and get rid of the residue and it just spreads it over the whole area so that the paint bubbles in an intermittent sort of way.
The only place it works is underneath fittings that are bolted or screwed to the boat - but ONLY on boats that will never be painted - even fibreglass boats may be painted one day - so what boats could they be?
Use a polyurethane sealer like sikaflex. It can be sanded, painted and it doesn't really cost much more. It also seals gaps in a structural way - so if the bits move relative to each other it will still keep on working.
In fact you can glue a whole boat together with sikaflex - not that I'd recommend it - epoxy does a better job in most cases - but there are places...
Disclaimer - if I sound bitter it's because of bitter experience. I worked as a professional boat painter and varnisher over several years - silicone sealant was the #1 reason for having to redo work that we thought was finished.
About the author:
Michael Storer supplies Wooden and Plywood Boat Plans for Amateur Boatbuilders. They specialise in Light, Elegant, High Performance, and Simple Construction. You can buy his plans with Detailed Step by Step Instructions by going to his website