If you carpet the inside of the storage areas make sure to leave a way for water to escape and make it back to the bilge pump.I like carpet inside storage areas to keep things from rattling around and getting damaged.The last boat I did decks on, I put the hinge between the lid and deck.Same as a door in a house.The guy that I did the deck for had someone unscrew the hinges(2 per hatch) and steel all his gear.Locking latches only work if the hinges can't be removed.If you wanna put the hinges on top,try to find small stainless steel carriage bolts, and use lock nuts on the inside of the storage compartment.They can still be drilled out,but I doubt a criminal will take the time.Hinges on top of the carpet help to hold it down and yea,I just drill carefully through the carpet.Sometimes the carpet fiber will wrap up in the bit and fray or pull up the carpet.When I use wood screws,I just run them through the hinge and through the carpet.Hope this helps.