I generally prefer short rods unless I am making long casts to cover water.
But, I fish shallow more than deep, cover more than open water, finesse more than power . . . so the advantages of a short rod from a kayak, for me, greatly outweigh a longer rod.
Accuracy, power, wielding/controlling/positioning the rod itself while seated . . . these are a few advantages. Big advantages.
One stated disadvantage? That a short rod won't clear the front of the bow if a fish swims across starboard to port or vice versa. This has literally never been an issue for me. And, for the few cases where I have to manage it, a big bass will take off directly under the mid-ships area of my canoe/kayak and, here, a short rod is much preferable to a long rod to control the fish. The extra power, too, means you can direct the fish a bit better as it comes in alongside.
One of my faves is a 5'6" M power St. Croix rod. It'd be my favorite. I rarely don't have it on board.