Just like current Worgen they would be in Wargon from 99% of the time. The fact that there are Night Borne has nothing to do with this. The same way Gilneas Worgen didn’t make an impact on Kul’Tiran Humans because they was already a second Human race.
So yeah. Night ELf Worgen would be WORGEN. 
The weapons were weakened but not broken.
I doubt there will be any more allied races for a few years at least.
If there were, though? I can think of a way to hit a homerun with the playerbase.
Undead Night Elves, let them name themselves like the sin’dorei did. Make it up. We see in 8.3 that they’re lost and looking to Calia Menethil for some guidance.
And for Alliance? I know this seems like something that’s not much different than what we have… but…
Quel’dorei.
Say what you want, but people would go nuts for them. For people who eyeroll, what if we let them be druids while we’re at it? They were into nature magic when living near the Wildhammers in lore, right?
I’d like to see one more pair to round out the expansion and fill in the character creation banners and the embassies. If they do intend to do two more I think Ji and Aysa going in the embassies as well as us returning to Pandaria is a hint of things to come.
My prediction is Jinyu (Ankoan and Pearlfin/Pandaria styled based on facial options) for the Alliance and Mogu for the Horde. The Waveblade rep could be used for the Jinyu and the new Rajani faction could be used for the Mogu.
This would also be a fair mirror to the reps of Mechagnomes and Vulpera where the Horde rep had been around longer than the Alliance one. This situation would be vice versa, though it is a relatively minor consideration either way.