Hi Karen,
No, the question numbers are not Theme specific. Question numbering is a tricky business, especially when dealing with client side code like Show/Hide logic. The best tactic is to hide the question numbers for those questions that are hidden (you can do this by advanced editing the question).
This has two benefits, it gets over the hurdle of questions not re-numbering properly due to client side computers. It also makes the hidden questions look associated with the trigger question since they are un-numbered below the parent question.
Hope this helps,
Chad