Don't install screws beyond your arm reach. I haven't seen it necessary to have perimeter line anchors or spare paddle bungies located farther than I can reach through the hatches.

If deck hardware screws are leaking into the boat they're DEFINATELY leaking into the wood core,,don't see why a person would allow that to happen to begin with given that the screws have to be secured well to handle the loads any holes through thin wood has to be sealed with eposy. I don't see the utility to mounting hardware at the very edge of the sheer to catch on things(sliding kayaks around during rescues). Given the varying angle of the deck to the sheer if one is using wood screws for deck rigging then the sheerclamp has to be wider and deeper than necessary for securing the deck/hull joint. 35' of extra wood to put hardware in a less than optimal position where some screws near the cockpit sheer might break through (because of the angle) doesn't make sense.

If one is building for long term reliability and cosmestic durability so the rigging screws can be installed and removed without damaging the wood there will be about the same effort spent drilling/sealing/re-drilling with machine screws through the deck or into the sheerclamp. Drilling into the sheer clamp you have to be pretty careful to not drill through or a wrong angle. When sealing holes in the sheerclamp it's a sequence of drilling, screwing screw in/out, putting epoxy in hole, not so much you have to re-drill, or you do and decide to attach screw while epoxy isn't completely hard with lubed threads.

If one is mounting hardware through the deck it's a matter of drilling through, putting masking tape on the inside, dabbing epoxy in the hole and watching it soak all the way in the end grain, then re-drill. Attach hardware when epoxy is hard.

the reason I developed a preference about this was re-rigging CLCs original demo boats in 2000 and finding one or two screws on every kayak was stripped and the kayaks with 1/2" sheerclamps had the 1" #10 screws poking through the sheerclamp in the cockpit. With machine screws and washers going through a solid epoxied core(drill,seal,re-drill) you know when the nut is seated down hard enough. With wood screws going through a hard skin(epoxied ply or glassed ply) the widest part of the wood screw shank is going through the hardest part of the wood and it's hard to tell how much of the seating is the compression of the webbing strap, resistance in the threads or scrw in hole.
Using a fullers bit eliminates some of that problem but I still don't see that mounting hardware at the sheer is optimum.