Caulking for deck frame
Maybe I'm just sloppy, but I've never bothered to caulk the seam on a doubled up joist with treated wood.  

There was one time I felt I needed to worry about that, but that was with a cantilevered deck using untreated wood.  In that case I just used aluminum flashing over the top of the joists.

I suppose if I were going to caulk it though, I would use a silicone caulk over a latex caulk since they generally adhere and hold up to water better (cleanup is messier, but it's a deck, so it probably doesn't matter).