Big things that go in hatches:

wheel carts
tent poles, fishing poles

Dry bags full of gear (like sleeping bags), extra floatation bags
Cooler

Your head and arm while making repairs

I think hatches can be very big without seriously affecting the structural integrity of the kayak. Especially if the lip is strong (meaning more layers of glass or carbon cloth) and heavier.
(This is not true for commercially made 'yaks that don't have the strength of wood core yaks.)

Smaller hatches probably keep their shape (curve) better and so are easier to seal.