Do you think that the actors used their puppets while recording the Avenue Q cast recording? (This is only half joking, I really can't picutre it any other way)
"I keep thinking about if you take the W in answer, and the H in ghost, and the extra A from aardvark, and the T from listen, you can keep saying WHAT but no one would ever hear you because the whole word would be silent."~Olive Ostrovsky- The 25th Annual Putnam County Spelling Bee
The answer is no, they didn't, but don't feel stupid for asking. :P I can definitely see their reasoning if they were to use them, as they rarely sing those songs without having a big ol' puppet in their hands. It might help character. :P
On a slightly related note: Last week at Broadway in Bryant Park, the sound check was sans puppets and the actress who plays Kate and Lucy kept putting her hands in "puppet position" while singing. I would imagine it becomes almost a reflex after performing these songs so many times.