I thought that perhaps given Madara's reaction to Tsunade, he may have spent his twilight years eliminating anyone of Senju blood whilst simultaneously carrying out multiple nafarious plots. After all, everyone needs a hobby right? *_*
Tsunade's self-imposed exile may have saved her... Maybe. I dunno, it's just a thought. But I think like other great powerful clans (Uchiha, Hyuga, Uzumaki etc) they were high priority targets for either elimination or capture from all of the other nations.
Other than that - I agree with much of the above, I imagine many/most died over the years in the Shinobi Wars - or married into other clans.
- B