Don't crap in your kayak. Problem solved
In seriousness, every 3-5 trips, I'll stop at the coin wash and pressure wash the whole rig, open up the hatches and spray with a bit of soap, then a bunch of water... Sometimes I'll just take it home and tilt it with the drain plugs down hill and run a bit of water through.... Once it's drained I'll put a big towel where the water pools and leave it for a day with the hatches open.