I figured their standing usefulness as energy sources may have been why they weren't employed in blue events so much but at the same time the other races are equally useful in other ways so I think it may have just been difficulty in coming up with things for them to do. So in light of trying to come up with ideas some spitballing.
As mentioned, preventing hacks from working.
Perhaps able to deal with Zoltan border patrol guards? Both those in asteroid fields who try to stop you for trespassing and maybe bypassing/benefiting the ship at crew checks for convicts? Preventing Zoltan aggression in the "confusion over your weapon's license" encounter?
Maybe positively affecting your encounter with the Monolith/eye encounter? "Your Zoltan shipmate, a devout follower of the ways of his people says a prayer in honor of the Great Eye to which the Monolith responds kindly"
Wowzers! I just found an actual Zoltan crew event! I've never run into it before.
http://ftl.wikia.com/wiki/Zoltan_Trade_HubAnyway, other things like that might be a good idea too. What with the official documentation and them likely being a citizen in the Zoltan government and thus able to get you through Zoltan events.
Maybe they could have an interaction with the Engi? Like at destroyed Fed bases your Zoltan could reactivate one of the less damaged Engi through funneling his power into the husk? Or maybe less macabre, but something.
This is the event I was referring to with the Rock ship, though if I remember my encounter correctly I don't recall ramming actually damaging their engines in any way.
http://ftl.wikia.com/wiki/Mantis_Ship_Rock_body_parts