If there is any core in the way of the screws, the screw holes need to be also filled with epoxy to avoid any water getting into the core. When you put the screws back in, you may want to put 4200 around the screw.
I have found that cleaning carefully with Magic Erraser "extra power" where the silicone was--this works very well--better than other methods I have used--you don't want to sand the gel coat. Silicone gets into the pores of the gelcoat--and then is difficult to fully remove.
Another trick is to not fully tighten the screws down when you put in the silicone--start with a bead under the lip--and then fill the crack--as the Silicone has set, then tighten the screws all of the way.
I wouold think that the primary reason to remove the deck hatch floor is to replace the fuel tank. If you can avoid taking the entire deck up, it might be a lot less work. There may be some screw holes under the deck which hold the fuel tank in place--maybe Andrew can answer this question--if there were straps or other fittings which were screwed into the bottom of the hull? If so, they should probably be removed and the area filled with epoxy and the screws put back in place.