I have never had a problem with water getting trapped in the frame, and my bikes have internal cable routing. I did have one extremely muddy race (pouring rain and 8 miles of the bike were on gravel) that I did on my road bike. The seat rails and post got completely gritty causing a creak, so I had to take those apart and clean them, but that has been it. If you are concerned, you might be able to put something like Glad Flexseal (or whatever that kitchen stuff is) over it. That should be waterproof but still allow cable movement.

Edit: I think it is called Press'n'Seal.