From the release notes:
Why was the startup preference removed? I really preferred DT not to open databases again on open.
You’re right. Looks like a mistake.
Most people expect them to be open on startup (as evidenced by Support tickets). Though I can’t speak specifically for Development, I could see them taking this approach since you can easily close the databases you don’t want to open on startup.
Not sure about “most people” - perhaps those of us who were happy with the previous behaviour didn’t file Support Tickets about it. 
Anyway, closing databases would be a lot easier if the option key triggered a “Close All” in the menu. I say that having just right-clicked my way through 9 databases that were open.
You could also have Command-Control-Shit-W’d your databases closed. 
“nuts’d”? My copy of DEVONthink doesn’t have that command 
ROFL!!! I have NO IDEA why that’s there!
It’s: Command - Control - Shift - W.
I quite like it - very expressive. Anyway, a curious point is that I can nuts all the open databases with that shortcut, except the final one. With only one database open, the File/Close Database menu item is greyed out. However, the context (right-click) menu still has a Close Database command, and works. An odd feature ……
We might add a hidden preference but a “Close All Databases” command is currently more likely.