Maybe they just all spread out and took different last names. Surely famous clans would have a good number of enemies. So they broke off, possibly after what happened with the Uzumaki-maybe. Or if the Uzumaki were massacred, the Senju, being allies may have gotten involved as well and lost some good numbers.
Uzumaki and Senju are descendant of Rikudou I believe. But everyone is scattered out.
1. Nagato in the Rain(?)
2. Karin who was orphaned young.
3. Tsunade, whose grandmother was an Uzumaki, but she didn't get the red hair.
4. Kushina, and later Naruto in the Konohagakure
5. Then you have Kinkaku and Ginkaku, who not only descended from Rikudou but have his weapons as well. Lord knows who they came from. Uzumaki or Senju is guessed. They may be Uzumaki, or descend from 1, after all, Tsunade, again, didn't have red hair. but she was still an Uzumaki family member. Though they have strong hints for being Uzumaki really.
I am thinking Senju, if not all dead have just scattered all over the place.