I'd use a good quality ('name brand'), new wood-cutting blade. It will be dull once you cut the opening if the deck has been glassed.
Something about 10 teeth/inch (tpi) or finer.
Some jigsaws have adjustments which affect the orbital action; check your manual for the setting for smooth (vs. rapid) cuts.
I don't worry about narrow kerf, since I've found that I always need to sand the cut edges to smooth them out and also to provide enough space for epoxy (and varnish) on the edges. You don't want to get a hatch lid jammed in the opening, and the waterproof seal doesn't depend on tight edges.
If you have some scraps, you could try the blade on those before cutting into the kayak. Start the cut with a line of (minimum size) drilled holes which you can join with some back and forth action with the drill - not the 'approved technique' but it works for me.
Something like this would be what I'd grab first: