Same issue, different Act. Right up to the end of Reaper's Coast, I had lower deck access. Hit Nameless Isle and the bug appeared.
I can go back to a Reaper's Coast save, and it works just fine. I have the same mods installed in both cases.
I can work around some things - put a work bench and anvil on the weather deck, for instance - but I would really like access to the stash and mirror.
This is, at best, a nuisance and, at worst, game breaking. A fix would be most welcome, devs!