a couple thoughts.....

first, i don't think you have to be concerned about reduced eficacy of using a buoyancy tank for storage unless you are storing water or lead.....i think the key concern is is the buoyancy tank going to stay secure and not flood....so that it can do its job and keep the boat from sinking or keep it high enough that whatever self rescue approach you have actually will work.

i think with some care, its not a big deal to make your own hatch.  that said, i have some strong preferences for hatches that have a very secure and visible indication that they are properly secured..particularly for any venture where your safety is really dependent on these tanks (like sailing beyond far from shore).  so if it were me, i probably would use the flush hatch kit approach https://www.clcboats.com/modules/catalog/product.php?category_qn=boat-gear&subcat_qn=kayak-gear-accessories&code=kayak-flush-hatch-kit or a similar approach using hand tightened nuts (wingnuts).  

i would avoid blind approaches (can't easily tell visually if they are secured) and err for an approach that is sturdy and capable of making very tight....(vs easiest to open quickly).

i also recommend positioning these hatches in such a way that they actually are above water when secured and the boat is flooded (vs positioning them in a way that they would actually be underwater).   no hatch is foolproof.....so risk is reduced by where the hatch is positioned in a flotation tank.

i have had hatches like these on small sailboats i used to own (like underneath a forward v berth).....and they worked just fine.

h

   Pretty much long the lines of what hspira recommends, I used the CLC kit to add flush hatches to the bow and stern floatation tanks of my Goat Islands Skiff.  The bow hatch is mounted centerline and will be above the water during a knockdown.  I had to mount the stern tank slightly off center due to support structure underneath.  If I get knoecked down to stbd this hatch will be high and dry but it will be partially under water to port.  If I had it to do again, I would have modified the structure so that the stern tanlk would also be on centerline.  

I agree with the comments regarding invisible hold down.  The flush hatches require a bit of force against the weather stripping to make a good seal.  I find that with about 8 toggles, they can be all but absolutely water tight.