I was playing Alpha Sector Virgilw.Aether. The Emitter on the hill to the south by the wall did not leave a power node when nullified. I do not think this was intentional.
I have not tried to reproduce this, but I believe that it occurred because the nullifier was destroyed by creeper the exact moment that the emitter was nullified. It was pretty close, and would be difficult for me to reproduce. Of course if that emitter is scripted to not give a node, that's fine too. However it's the only emitter I've seen to ever do that.
Well, there are definitely custom maps out there with emitters that do not leave power emitters, although I don't know if that particular map is one of them.
Seems like it's working to me. Although, something might've gone wonky in your build. Which version do you have?
Newest one, just downloaded it. Like I said, it's hard for me to try to reproduce it as the emitter just finished firing the second it died.
Edit, just looked it up, 1.63 is my version. Since my first play on that map, I did in fact get a power node when I nullified that emitter. Just not the first time.
Your explanation is probably what happened... that sounds extremely difficult to reproduce though, and at least it isn't game-breaking.