I share you concerns, but, took a few steps to make me feel better.It's difficult to see in this old pic and I have replaced since this was taken, but, I used a whole tube of silicone caulking inside and out of the hole where the cables run through to seal it up. I haven't had any trouble with water coming in. I also have the bulkhead on the front edge of the splashwell to keep the water in the well. I keep the plugs in while on the water. The water that does get into the deck area goes through the livewell in the floor and I turn on the bilge pump once an hour as a precaution.
When I get around to replacing the transom, which isn't necessary right now, I'm going to take some additional steps to fix these issues, like raising the transom to 25" and the floor a couple of inches including the bottom of the splashwell.