I was just wondering if the Downstar Dark Brotherhood Sanctuary's master bedroom had safe storage?

Yes. I used the chest, wardrobe and various end tables and never lost anything.

Dunno why you would want to, its so grubby and disgusting down there, at least the old sanctuary wasn't such a mess...

I've kinda' wondered about this myself. I assumed it was since I'm also assuming that the Master Bedroom is ours. I replicated a set of DB Shrouded Armor and store it there, plus I put a Dibella Statue (my assassin is a chick) by the bed. So far the statue is always there, but I haven't checked on the armor.

Fix the place up and you'll get a dummy and weapons rack. I think a chest as well.

Is there a mannequin? I never noticed.