We need more facts to evaluate you wife's case, since your case is already before the Judge, you need to personally review your case with an experience immigration attorney. I have an office in Tampa if you wish you can contact my office.
You and your wife need an immigration lawyer to advise and represent you. See the AILA link below. Yes, if your wife departs the US, she will be subject to a three year bar to reentry at this time, because it has been over 180 days since the NTA wass issued. Once a full year has passed since the NTA issuance, she will be subject to a ten year bar upon departure from the US. She should not request VD until she is represented by an immigration lawyer who advises her to do so. Yes, the court wait time counts as unauthorized presence for the three and ten year bar purposes. If proceedings can be delayed until you are a US citizen, your wife has a vrery good chance of being able to stay in the US as a permanent resident.
You need to show the NTA to a lawyer who does removal defense work asap. Call some immigration lawyers and tell them the facts of your case. Although some will tell you to pay for an in person consult, many will give you a free consultation on the phone. You will need your wife's entire immigration history and the NTA in front of you while you call. At this stage, it is very important that you not make the wrong decision. Start calling asap... do NOT wait until the last minute.