It's a risk u have to take n i guess everyone is taking. One of my friend who had worked on ssn for more than 6 months had no issues getting GC while staying in US. N looks like lots of people have gotten through with no issues. However uscis definitely talks about potential problem in adjustment of status with 180 + of unauthorized work. If you mention ur wifes work on the application, that would definitely raise the red flag, however if don't mention it, they might not find. There r cases when uscis has sent RFE for unlawful presence. It could be like they will randomly audit an application for the work history based on ssn and find some. So u can apply without mentioning the work and hope for the best.
The other option is that ur wife will got out of US and come back on F2 and apply therafter together.

For EB3, current priority date is April 2011 which is i140 receipt date. Considering 8-12 months for other steps till i140 application, total wait time is 4 years which might vary. For updates see. http://travel.state.gov/content/visas/english/law-and-policy/bulletin/2014/visa-bulletin-for-july-2014.html