If a woman is widowed or divorced, she must wait long enough before remarrying to firmly establish the paternity of a child who might be forthcoming (Daily Halacha cites SA Even Ha'ezer 13). The purpose of yibbum, though, is for the brother to father a child in the name of his deceased brother (Devarim 25:6). In that case, the paternity question might not be relevant -- either the child she is carrying is the deceased's or it is the yibbum's but as if it were the deceased's -- does it matter which? There might be other reasons to need to know (in modern times, medical history for example), but in terms of halacha, does the yibbum still wait 92 days or may they marry sooner?
If the child is the deceased brother's, then Yibbum does not apply and the brother-in-law and her are biblically forbidden to marry each other. Thus, they must wait (ShA EH 164:1).
Paternity is also important in determining who the child is related to regarding Arayot, in cases where the husband and brother are of different lineage (eg. the husband was a Kohein but his brother is a Chalal), and for determining inheritance procedures (eg. for the estate of the husband (does the son get all of it or does it go through the brother and eventually be split among the brother's sons) or of the husband's father (does the son claim his father's half or does the brother claim it all and have it eventually get divided among his children)).
Yevamos 41a - Mishna says that a Yevama should not do Chalitza or Yibum until three months have passed. Thus the waiting period is applicable also in a case of Yibbum.