1. They pause to contemplate whether they are really in fact, stupid. They think to themselves gosh lately I have been doing a lot of dumb things, and...well what I just did right now caused this other person to become concerned (ie: angry, mad, frustrated) enough to genuinely wonder if I am in fact stupid.
2. They pause because they are confused and trying to figure out if this is one of those times where people don't actually want an answer to their question but are asking you anyways. They become momentarily paralyzed while they debate whether or not to answer. Which if they have to wonder whether or not answer a rhetorical question, the answer to your original question is in fact, Yes.
Either way, their stupid actions caused you to have to actually ask if they were stupid because it was so convincing and for political reasons you needed to clarify because if you carried on attacking them after they admitted to being stupid then it would be just as wrong as telling a retarded person they were acting retarded. As long as the "questionable stupid person" claims he/she is not, it's game on! Stupid!