It has just be brought to my attention that a commonly asked question when redding a Shidduch is if the mother had gone to the Mikvah or not. Is there a halachic problem if as a Baal Teshuva the mother did not go to the Mikvah? Is this a legitimate concern?

It is wrong to deny the children of Baalei Teshuva or those who are Baalei Teshuva themselves the possibility of marrying into religious families. Such a policy would work to discourage Teshuva (see Shu”t Chelkat Yaakov Even HaEzer 11). HaRav Moshe Feinstein’s conclusion in dealing with this specific question (Iggrot Moshe Even HaEzer 4, 14) is that a person who is observing Torah, who is of good character and who is G-d fearing can be assumed to be the son of someone who was not a Nidda (perhaps without any religious intent his mother bathed in the ocean or a lake prior to his birth). There are many considerations- love of Torah and the Jewish People, fear of G-d, idealism, compatibility- that are much more important in finding a Shidduch than the consideration mentioned in your question. I suspect that putting a misplaced emphasis on this kind of factor diminishes the importance of what is really essential and sidesteps the need to address real questions of personality.