On Ancestry's online tree system, one option is to create Weblinks between the two profiles. The disadvantage of doing it this way is that Weblinks aren't synced with Family Tree Maker.
Another possibility, mentioned in the previous answer, is to link them by their surname if they have a common surname.
Crista Cowan has said in her Barefoot Genealogy videos that users can indicate unknown names by using five underscores. That won't disrupt Ancestry's hinting or search algorithms.