At the moment, no. Though, after 2.0E is out, there's plans to redo the stats of most of the ships in order to accommodate ion cannons. The reason it hasn't been done yet is that this will pretty much turn the entire mod atop it's head. I'm also thinking, as an additional passive ability, to add in a bit that if the shields of an enemy's ship is down, for the ion cannons to have a high, or guaranteed, chance of partially weakening a ship, like the ion abilities already ingame, but far weaker. However, the upside of this is that these bits will pile up with multiple ships, and can possibly mean the end of a ship.

I've also wanted to do such a passive ability, but the problem is I'm not sure if there is a sure fire way to only apply a buff when shields are down. Indeed, if Sins shield regeneration is constant instead of per second the only time shields are completely down is immediately after a normal weapon hits.

From my understanding normal shield recharge adds shield points every few seconds in a lump sum, not constantly.  Abilities that restore shields apply every half-second from what I've seen.

There is an if shields are down finish condition, ShieldFailure. So it'll have to use that... I imagine it'd have to make use of a "check" buff, that is the weapon sees if the shields are up once it hits, and if so, apply the ion thing. I'll admit I'm not entirely sure how to work this out, but it's a start. Edit:

This is true, the devs did this in order to discourage focusing fire.

Oh yes there is.  I've done it.  It's a rather complex buff, but I've done it.

Before I go about taking a stab at this, may I have permission to use parts of the Grey Goo in order to get this ability coded? You of course will be credited accordingly.

Sure 

The ability infects only those ships whose shields are down.  It spreads to other ships without shields.  When the ship dies, it spreads to ships in a larger radius, regardless of whether or not they have shields and it also spawns a nano cloud (but since I fail at importing models, I just used the TEC missile turret).

With a buff that overly complex, I figured a little explanation might help lol.

So I noticed, it's one heck of an ability that's for sure.

Main bit is the shields down part; in a nutshell I'm hoping to work that into a passive ability that's linked to Ion an weapontype that fires, and after some complex thing that checks if shields are down, applies a buff.

Probably what you'll want to do is on BuffGreyGooTarget, replace the BuffGreyGoo on the ABTS with your buff.  IIRC, you'll need BuffGreyGooShield, BuffGreyGooTarget, BuffGreyGooImmunity, and your buff, but I haven't looked at it in a while, so I may be mistaken.  Look for the Darkness Mod.  That's what I made it for and there's a detailed explanation of the files in there.

Found something else that would be nice. Order delay. So that once an order is given, it can take more or less time for a unit to actually follow that order. This would be IMMENSILY helpful for some of the stuff I'm modding in, as well as be good for a jamming ability.

You're looking for the instantActionTriggerType "OnDelay". Link.