Would a neutral nature be more benificial to a Zen mode Darmanitan or a Quiet/Modest nature be better, those natures would hinder in normal mode but help in Zen.

It depends on which type of darmanitan you like if u want a defenseive one remeber it isn't always defensive . This always applies because of zen mode activating and deactivating. If you want it to be a sweeper get a speed boosting nature or attack boosting.

If you just want the zen darmantitan, give it substitute. to cut its health down. And a modest nature, i have a similar set up to this.
Darmanitan @Petaya berry
Modest nature
-substitute
-fire blast
-focus blast
-psychic
hope this helped