You could try going in to a store, we can check on registered devices (we can't deregister them any more than you can) and call a different group of support to try and deregister it.
I would suggest going to your local B&N, finding the Nook person, and explaining the situation. I would suggest doing this soon since once the holiday is upon us time gets a lot more demands placed on it.
You can also try PMing Alex, if it's the only NST registered to your account that you don't have access to he may be able to help. You'd likely need to provide him with the SN's for the NSTs you have and want to keep registered. Giving him SNs for all the Nooks you have and use may actually be better.
...but I have a broke one counting against my registrations.
I don't believe B&N limits you on how many nooks you can have registered to your account.
But, yes, I agree, it's annoying to have them listed. I wish they would let us, at least, "hide" them like Google does (or NAME them so the list says "Dad's Nook," "Dead Nook", and such).
You should be able to deregister your dead nook under your account. Go to Manage account, once you are there scroll down to digital content and you should see manage your nook and you click on that and you can deregister your nook from there.