Similar Experiences here
I have a Bavaria 36 - a similar boat, and have had similar experiences with mine in the past. When new, we had water in the small bilge just forward of the engine at the base of the companionway stairs. But that was fresh water, and we concluded that it was from a very bad storm.
If you dump water into the compartment behind the engine (not into the small engine bilge directly below the engine), it will find its way to the forward bilges. The most likely way salt water can get in there is from a raw water coolant leak, from a hose, fitting, or the anti-siphon valve. This water will likely not go into the engine bilge, but travel around it.
Yes, you can get salt water via thru-hulls not closed off, but (in my experience) only under darned aggressive sailing. We always leave those open, frequently get heeled to 25-deg, and have never had water come in there. I doubt this is your problem.
On our boat, but no others that I know of, there was a failure of the heat exchanger that let in raw water. If that were the problem, you would get an increase in coolant level to overflow as raw water leaked into it, when warm, followed by a decrease in coolant level when the system cooled down again - and it might be a while before you noticed signs of such a leak on the engine block. Yes, it did happen!
The chance that water is entering the boat past the deck-hull seal is extremely small - that seal is redundant. Also, you would have to sail very aggressively - lots of heel, lots of spray to get significant water to that level for a length of time.
Water coming in past a bad saildrive seal would find its way into the engine bilge - but this is easily checked - the rubber seal will have trapped some and still be wet.
I believe a bad rudder suspension will not leak into the boat - but not sure. If it did - that water will find its way to the main bilges.
Finally, on Bavarias, the hull stiffeners are all vented - that is, they have large holes in them to allow water to pass. Only a small amount can get trapped in there, and most of that will find its way out.
Hope this helps - keep looking - let us know what you find
Ken