@tanguatlay,
The phrase "since then" is needed, if the meaning is to be conveyed that it has been passed down since the time of the Tokugawa Shogunate. It would depend upon the time of the establishment of Nichen Shoshu (some of which i am obliviouisly ignorant). When Tokugawa Ieyasu defeated Takeda Katsuyori at the battle of Tommokuzen, in 1582, the Tokugawa era can be said to have begun. There was little effective resistance after that, so i believe the Tokugawa Shogunate can be dated as early as 1600, although i don't believe he was formally invited to be Shogun by the emperor until 1605. I've read of it dated to 1624 in some sources, although i don't recall why.
So it turns on the question of when Nichen Shoshu was established. If that was around 1600, around the same time as the establishment of the Tokugawa Shogunate, than the word "then" is not needed, but since is needed in either case. If Nichen Shoshu was established well before 1600, then "since then" is needed to indicate the time since the establishment of the Tokugawa Shogunate.
What the hell is Nichen Shoshu, anway?