Should I Have Everything Else in the Game Done Before Playing Citadel?
There is no right or wrong time to play the Citadel DLC, once it’s unlocked. If you play the Citadel DLC with everything else unlocked (just before attacking Cronos Station), the new DLC content will all be unlocked. If you play the Citadel DLC right after stopping the Cerberus coup attempt, the DLC content will unlock naturally over the course of the main game.
Does the Citadel DLC Affect the Ending?
No, not beyond the possibility of adding new war assets to increase your Galactic Readiness score. You may of course continue on to play the endgame after completing the Citadel DLC, but there is also a natural “stopping point” that should make it clear where the DLC content ends and your return to the main game begins.