Nope, sorry.. upgrades can only effect 'base stats' and skills. Effects/Emanations are getting a tune up in 0.3 (but probably not in time for the initial release), so I'll look at adding this ability then.
The differing effects for different unit types is, as John pointed out, not possible either, but will be vastly more simple to implement, so I think we can probably squeeze that into 0.3.
Cheers.