I think it's well agreed upon that 3D does not fall under traditional roguelike standards. However, as the main page states:
You are challenged to create a game that features gameplay that is:
Turn-based, focusing on strategic thinking over quick reflexes.
Run-based, with no meta-progression (the player loses all tangible progress after each run).
Subject to permanent consequences (the player cannot freely roll back mistakes).
Impacted by Procedural Content Generation in a meaningful way.
Focused on the development of A character, or a party of characters (no abstract puzzle or "god" games).
So that leads me to believe 3D is welcome? But probably wouldn't earn any brownie points from people "expecting" a traditional roguelike...
The theme is whatever you want if it follows the above.