It will take a bit more force when the glass is on, but it should still be quite easy to close a 1/4" gap.

In any case, that 1/4" will almost certainly change as the glassing is done. It could get better or worse. The hull and deck often change shape slightly as the resin cures. You can reduce the extent to which it changes by avoiding a big delay between glassing the outside and the inside. It also helps if there is not a big change in the temperature and humidity in that time. It is also a good idea to use either the forms or spreader sticks to try to keep the hull and deck close to the original shape while you work on the other half of the kayak.

It should not be a problem if you can keep the gap near 1/4".