“MY son is going to marry an Irish girl who has been living here undocumented for six years. He is American. I am concerned that her status will be held against her when she applies for a green card. Is this so?”
No. As your son is American, your future daughter-in-law will be able to apply to adjust her status while still in the U.S., via the USCIS.
The period of illegality she accumulated will not be held against her at all, which is one of the reasons why it is advantageous to marry an American citizen (love being the first and foremost reason, of course!)
Still, it would be wise for your son and his future wife to consult with an immigration attorney to file the adjustment paperwork and receive advice on how to proceed when interview time comes.
It is critically important that she remains in the U.S. during the adjustment process. If she was to leave, even with an approved advance parole document also available from USCIS, her undocumented time in the U.S. would likely be held against her, forcing her to wait abroad for final processing.