Vincent might not have actually been romantically involved with Lucretia. They were close, and mutually attracted, and although Vincent loved her, that fell apart (for reasons detailed in Dirge of Cerberus) and she rebounded into Hojo's arms and an obsession with her work. Vincent's a smart guy, and likely would've known if there was a good chance of him being Sephiroth's father. He was sealed in a tank during her pregnancy, and saw the worst of things for himself. It's true that Sephiroth's originally cool demeanour and his good looks give him more in common with Vincent than with Hojo; however, Sephiroth's nature seems to be predominantly due to characteristics inherited from his "mother", Jenova, rather than his human mother and father. The flowing silver hair and inhuman eyes are a giveaway.