Naughty would work best with Hoopa-Unbound.
Neutral natures, such as Hardy and Docile, may not seem so bad on paper... but you're actually not benefiting from anything. You're not sacrificing anything, but it's better to gain something. Many Pokemon are one-dimensional, meaning they tend to prefer one stat over than the other. Natures that are not neutral can give a 10% bonus to a given stat and a 10% decrease to another stat. This can really add up later on.
Timid isn't really an optimal nature for Hoopa-Unbound because it likes to run either a Mixed attacker set or a Physical attacker set. Lowering the Attack for gaining Speed would not be helpful in this case.
Naughty nature would be the best because it doesn't lower either the Sp. Atk or the Atk and raises the Attack at the cost of Sp. Def (which Sp. Def wouldn't be as important as the attacking stats).
You could use the Timid nature Hoopa for a normal Hoopa set, so I will also post a set for that.
Hoopa @ Salac Berry / Leftovers
EVs: 4 HP / 252 SpA / 252 Spe
- Nasty Plot / Psyshock
- Shadow Ball
- Focus Blast
The idea of this set is to keep on using Substitute + Nasty Plot until you get around 25%, so you can gain the boost from Salac Berry. Leftovers is also a nice alternative. Shadow Ball + Focus Blast grants near perfect coverage and Psyshock deals with special walls and gets STAB.
Hoopa-Unbound @ Life Orb
EVs: 68 Atk / 188 SpA / 252 Spe
- Drain Punch
- Hyperspace Fury / Dark Pulse
- Gunk Shot
Standard Mixed Attacker set. You can also try a Banded Hoopa-Unbound set with Hyperspace Fury / Gunk Shot / Drain Punch / Zen Headbutt with 252 Atk / 4 Def / 252 Speed.
Anyways, that's all! Hope I helped.