I was never able to implement a Nuclear Bomber in my own mod, but I see there IS one now in the Conquests WWII Scenario. Anyone used it yet? How exactly does it work? Can I implement it in my own mod just by making a link to the appropriate folders, or is it somehow hardcoded in-game?

The problem I always had was that Nukes have their own attack animation which wasn't compatible with the "fly-by" normally used in Air Bombing missions.

How has Conquests overcome it?

The nuke in conquests is the famous A-bomb of WW2 and the attack animation is a plane (B29?) dropping it.

Does it still do damage as a Nuke? Every unit I've ever checked as a nuke had the vertical launch of an ICBM, then dropped down on the target.

A B-29 actually flies across the target and drops a classic A-bomb? You get a nuke explosion and everything?

Yes. The unit is the nuke the B29 is just part of the animation and is not a seperate unit.