I had a several ideas about improving HN a while ago (some for strengthening, some for nerfing). I don't remember all of them, but here are a few:
Strengthening:
HN units could take cities (even while at peace with the owner), but must raze them.
A shadow spell (and possibly pirates coves) could grant the HN promotion.
The declare nationality ability should not include the cancast(caster) or docast(caster) statements, so nationality can be declared right before attacking or after casting (and so that HN summons can declare nationality and still do something for those who do not have the summoning trait)
Possibly, HN units could be made able to attack your own units, so that you can convince other players that the unit must really not be yours. If this is added, there should really be a way to stop them from attacking friendly units when automated (perhaps automated-exploration units should just not attack at all, but just stop when they are near an enemy. Automated Scouts dieing when they stupidly attack stronger units is also kinda irritating)
weakening:
A sun sphere spell could remove HN from a unit, forcing the unit to leave your boarders. This might also hurt the diplomatic relation between the civs.
HN units (especially when attacking) could be caught (kinda like spies). The equivalent of catching but not identifying the spy would let them eject the HN unit from their boarders and would let them suspect the nationality. Usually this would give them a diplomatic penalty towards the units owner, but occasionally (especially when you attack an enemy right after leaving another rival's boarders) there suspicions would be wrong and the wrong civ would be penalized. The equivalent of catching them and discovering nationality would give a larder diplo penalty and force the HN unit's owner to declare war whether he wants to or not.
The chances of getting caught are much higher if you raze a city, if you have non HN units on the same tile, or if you attack directly from your cities/territory.
HN would not allow multiple attacks per turn while at peace (I assume you would fix this soon anyway)