If you think you will never have to take them out again you can epoxy them in with a two part epoxy such as Sea Going epoxy. It is available from Rex Marine, Glenwood, or Bergeron Engineering. If you think you may take them out again I would try SikaFlex. I have also used regular silicone to seal up bolts that are going through the hull, easy to remove but also least reliable and least permanent.

Brian