Lauri,
If you have the original hatches, they were installed with ordinary household silicone for bedding. Silicone contains some oils that tend to penetrate the fiberglass & gelcoat, rendering it difficult/impossible to get good adhesion with other sealants. The good news is that there is no exposed deck core, so you won't have to deal with a rotten core.
My recommendation is to stay with a silicone, but use a commercial grade construction silicione such as Dow Corning 795. Ordinary silicone has great flexibility, but almost no adhesion strength. Thermal expansion and contraction quickly breaks the seal, eventually resulting in leaks. DC795 has both flexibility AND substantial adhesion. Its used as the sole glazing material to hold in plate glass windows on hi-rise buildings. It does require about a week to fully set up, and should not be stressed before that time. I used it on my hatch rebuild project and it worked great.
