Looks like there will be plenty of opinions on this; I've heard tell that opinions are like A-holes :) Everybody's got one. I don't think there are any right or wrong answers, so I'll just make a few obsevations.
No matter how well sealed you think something might be, I wouldn't trust a permanently closed, unventillated compartment in a wooden boat. More power to Laszlo for the success (luck?) with his wife's kayak. I've seen (and sometimes tried to fix) dozens of cases of rot in all kinds of boats - everything from balsa-cored hulls and decks, plywood cored transoms, varnished wood boats, etc.. Rephrasing a line from Jurasic Park - "Rot will find a way."
I've done end pours both ways - and of course contruction methods and bulkheads/hatches dictate the possibilities - standing the kayak on end after deck was on, and also horizontal prior to deck installation. In all cases I think the epoxy should be well-thickened to make it cheaper, lighter and less brittle. I used microballooons - but wood flour would seem fine, too. I'm sure a wood block would work and be cheaper - but seems more work to fit and install than just pouring in a cup of epoxy, and with epoxy you don't have to worry about ensuring a waterproof coating of the inside of the handle-line hole. I learned two lessons: One vertical end-pour (on a 100 degree day) cooked so hot it speckled the deck/hull glass. Prior to the second pour I stood the nose of the kayak in a bucket of water (and even swished the water around) to keep things cool. When doing a horizontal pour with a dam I inadvertently left a place where my duct tape had a wrinkle - the resultant leak was a mess - I kept adding tape trying to seal things up - but it didn't stick well with all the goo already flowing. I put my finger in the dike for about a half hour and begged the epoxy to start setting up! Luckily I had NPR on the radio. (And I'm glad I'll be the only one to ever see the mess made in that part of the kayak again.)
Based on my usage, I personally would never go without hatches, but that's because I store things in there. However, like you I think the multi-strap hatch closures on some CLC styles leave something to be desired aesthetically. It took more work, but I've made my hatches flush and used invisible hold-downs (bungee) from underneath - both on flat Shearwater hatches (easy) and curved Chessapeake hatches (more difficult). I expect a bit (teaspoons after several hours) of moisture to get through the seals in a capsize or constant waves breaking over the kayak, but that's all. If my use was in whitewater or really out at sea I might want something more secure.
My plastic (abuse-proof) kayak has only styrofoam chunks in the ends. When I use that I throw things in a dry bag with a light line attached. I kick the bag all the way up in the bow, but can pull it back to my lap when I need lunch or sunscreen. The kayak does have a larger sized cockpit opening.
Bulkheads make sense to me for both floatation and structural reasons.
So now that I've made all the observations I can't resist offering opinions. I would put in the bulkheads. Then decide if you want to put hand-ports in the bulkheads (ventillation and mini-storage) or "invisible" flush hatches. I think the hatches would be only slightly more work, but would add flexibility.
Whatever you choose will be the right answer for you. And if you change your mind, build another boat!