Silicone caulk has no place on a boat. Over time it is permeable to water, and leaves a film on the fiberglass that is almost impossible to remove. You need to remove all the hardware, remove all silicone caulk (and residue), and re-bed properly. Don Casey's Complete Guide to Sailboat Maintenence is an excellent reference, and one that any sailor should own. I have never read This Old Boat, but I would assume it is similar.
While this is a small leak now, do not take it lightly. This can quickly turn into a MUCH bigger problem (rotten core) it not fixed quickly and properly.