If I enter the Black Flag lower deck where Jak Silver is, there is no exit available and I have to reload a save game to continue. Even Jak Silver himself is constantly walking against the wallI trying to get out. Is this a bug? I can't find any trap door or ladder leading out of the lower deck. I have installed all the official and unofficial patches including the unofficial plug-in patches.

I had to look at your username a couple times to make sure that I hadn't posted this in my sleep. I was going to post the exact same thing this weekend. Same situation, I have all the patches and unofficial patches. I have to use a coc console command to get out.

What console command do you use to exit the room? Is there a command to force Jak Silver to exit together also?

Well, I just type 'coc anvilmagesguild' for example to get out. You can find a list of valid location codes somewhere.

I've experienced that thing with Jak Silver once. There are a few location codes for the Thieves' Den. The main one, dldunbarrowhaven, puts you right in front of Melliwin where she's doing her archery practice. But one of the other ones put me into the ocean, under the ship, and Jak Silver looked like he was treading water or walking into it or something. I haven't tried that one again.

Here's the wiki link that shows the location codes: http://www.uesp.net/wiki/Oblivion:Dunbarrow_Cove_%28place%29. I think the 03 one was the weird one. I think the 02 one puts you in the Captain's cabin.

I have found the solution for this problem. Open your Oblivion launcher file and select Data Files. Uncheck the DLC-Thieves Den Unofficial patch SSSB.esp.
Apparently this patch fixes a door opening sound by changing the Black Flag's middle and lower decks but messes things up instead.
After unchecking this patch, ladders and trapdoors appear leading to the upper and lower decks. I didn't even know that the lower deck is accessible.