I can understand your wish to consider all possibilities before you cut a couple of huge holes in your carefully crafted kayak.

In my case I considered a couple of other things as well as the things you have mentioned.

I thought it would be handy to be able to reach more or less to the extremes of the cargo area, so that put it about halfway between the bulkheads and the ends.

I also wanted the cutout to follow the strips that created the pattern on the deck.

As a consequence, my hatches are a bit smaller than many I have seen.

However, that is not a problem. They are plenty big enough for the gear I put in there and I figure the kayak is stronger for having smaller holes cut in the deck.

That doesn't exactly answer your question, except perhaps to indicate that different sizes and locations might suit different people's needs.