Steel, wood expands and contracts with changes in moisture. Right now the unfunished rudder absorbs water when you're sailing and dries out when she's on the trailer. That's why you're getting some cracking.
The idea is to seal the rudder, that will slow the rate of expansion and contraction and prevent any future cracking, and will fill the existing cracks .
Since she's been bare wood for a while and you do have some cracks I would sand her back a bit with 80 grit on a random orbit sander. Keep the sander moving. This will remove surface grit and the rough gray wood.
Make a filler paste using the sawdust from the sander's dust bag mixed with CPES and use it to fill the cracks. Mix the filler to the consistency of peanut butter. Then coat the rudder with a couple of coats of CPES to seal it. Here's the link for CPES
CPES doesn't have UV inhibitors so you'll have to paint or varnish the finished rudder. It's also forgiving on the mixture ratios.