Absolutely. Pet peeve of mine. Seems like a waterproof seat compartment shouldn't be too hard to do, small lip molded into the seat would do it.
Anyway a couple of things to check from my experience:
1. are your drains on the top of the seat lined up? In the groove on the top of the seat compartment there is a drain hole. That needs to line up with the part below or it actually funnels water into the compartment. I had to put a small stainless screw in some of them to keep them lined up.
2. are there drain holes in the bottom of the seat compartments to let water out if it gets in? Mine did not have any so I drilled some. Before I did that after a rain storm (if the cover wasn't on) it was not unusual to have 3-4 inches of water in some seats. At least with the holes most will drain out. I very carefully drilled 1/2 inch holes in the sides of the compartments as low as possible on the stern side. The boat naturally floats higher in the bow so when it rains water won't wash into the holes.
Other than that it is vigilance. If the mooring cover is on I don't get water in the seats. If it rains without the cover I take everything out, dry the compartment and let the life jackets air dry before putting them back in. In the sun it only takes 1/2 hour or so.
Last year my boat was delivered from the marina and there was water and mold in all the compartments. So if you don't take care of it it will be an issue.