All Naruto fans have great affection for many of the characters that appear in the popular Naruto and Naruto: Shippūden anime and manga, so we can often see them delve into the lore of the story, especially related to to the beginning of the ninja world.
Something that seems quite striking to us is that the Senju clan are the direct descendants of the Sage of the Six Paths, who spread chakra throughout the world. They were one of the strongest clans during the Warring States Period and co-founded the Village Hidden in the Leaves along with the Uchiha clan.
Despite its great importance, the clan seems to have disappeared at the beginning of the Naruto anime. Unlike the Uchiha and Uzumaki clans, who were massacred at the start of the series (or shortly before the original events), it is never stated how the Senju clan was wiped out. By the time the series begins, the world of Naruto had already endured three Shinobi World Wars in a relatively short period of time.
These were massive conflicts that involved all the hidden peoples and led to the deaths of thousands of ninjas. Several members of the Senju clan are known to have fought and died in these Shinobi World Wars, Harishrama Senju and his brother Tobirama Senju fought and perished in the First Shinobi World War in Naruto, Tsunade also participated in the Second Shinobi World War, her little brother Nawaki He died in this war.
In fact, a known member of the Senju clan has been a part of almost every Shinobi World War and died in the conflict. The Senju clan may have lost most of its members during these wars. They would have been pushed to take on the most dangerous and important missions due to the recognized strength of their clan.
The Senju clan also developed the Will of Fire philosophy that prioritized the safety of the village above all else. It is not uncommon for powerful clans to be targeted for kidnapping and assassination in the world of Naruto. Many towns and clans fear powerful ninjas and covet their secret jutsu.
There are multiple instances of coordinated efforts to kidnap children with strong kekkei genkai or slaughter clans that are known for their strength. Orochimaru spent several years trying to take over the bodies of Sasuke and Itachi Uchiha so he could have the Sharingan from him.
The branch family of the Hyuga clan is marked with a curse seal that ensures their Byakugan is locked away upon death. Hinata Hyuga was almost kidnapped as a child by a cloud ninja. The Uzumaki clan and their homeland were wiped out due to their ability to seal jutsu, with this we can conclude that, being the most powerful clan, they were targeted by everyone.