With the San Juan Island you have several choices - note these are choices, not rules. If I’m landing on an island or paddled to beach, I know I’ll be leaving the boat at the shoreline - or rather way up from the shore line. But at the County Park - what with lots of vehicles that carry boats - I’d be driving down from my campsite, unloading the boat, and paddling about. On return, I’d reload the boat on the car and drive back to the campsite.
Now if I left from the “boat launch area and drove my car back to the campsite, I could land at that small beach down the stairs from the dedicated Non-Vehicle camp area. In that case (no direct car access) I might leave the kayak on the beach for the night but I’d be real sure to check tide levels, store it as high as practical, and tie it off.
If you were going to leave them at the vehicle access point, maybe you could use a cable to padlock them together.
I do have faith in my fellow person and was raised in a home/neighborhood were we didn’t lock our doors. But I also know what can happen if you leave a plate of cookies in the lunch room.
It’s always good to check with the staff. You’ll know their preferred policy and they’ll have a visual connection between you and your boat.