E39 - Anyone had problem with water near Companionway Hatch?

I don't know if this exists on any other boat, but...
My E39 (1976 flush deck) has a sealed compartment where the companionway slider hatch slides into (like most sailboats). The problem is that rainwater also disappears into this recess, from either side of the hatch (opening is about 1/2 inch either side and on top of the hatch itself).

It looks like, at one time, there may have been weep holes port & stbd of this recess, about 1/2 inch diameter, but they were caulked up and epoxied over long ago. We discovered these while doing significant core repair in this area from underneath. It's possible that plugging these holes could have caused the problem in the first place, but what problem would have caused someone to plug them up???

If these were weep holes, they don't seem to be ideal, as they could allow water that splashes onto the deck drain INTO the weep hole from the outside while underway. Perhaps I'm missing something though.

My questions: 1) Does anyone else out there have either these weep holes or have problems with water draining into the companionway slider hatch recess? and; 2) Any thoughts on how best to keep this area clean & dry?

I'll try posting pictures next time I'm at the boat. Thanks!

we had a little seepage from the sea hood on our 38 as well. I'd suggest taking it off, cleaning up real good, rebedding it, then sealing all around the joint where it meets the deck. The seep holes seem useless to me, but maybe somebody has a better thought. Since rebedding our seepage has stopped completely. Get this done before you do too much core repair, otherwise you'll end up doing it again...
Chris

ps. should be a thread about this somewhere here with really good photos.

I'd love to do that, Chris, if only it was possible. Most newer boats have sea hoods (thank you for reminding me of the proper name) that can come off and be rebedded. The E39 sea hood is an integral part of the deck and cannot be removed.