(I'm cc-ing the list because I thought this might be of interest
to others.)

I wrote:

My brother, who first informed me that Jubei (as well as the
other two main characters of Ninja Scroll, the poisonous
kunoichi and the aged sensei) is a historical/mythical figure,
described Jubei as a younger son of a Daimyo
(and so entitled to wear the two swords, though he only 
seems to wear one) who runs around disguised as a ronin, for
no particular reason other than it being a handy way to
encounter adventure.

Ridgewolfe wrote:

Oh really???Is there any way that you could tell me where to
find out more about the historical characters?  I need background 
material for a fic i am working on...

Sorry about the delay in responding to you.  I sent my brother an email
and he never responded, so I finally called him today.

Anyway, here's what he said:

The historical Jubei was a younger son of the Yagyuu family,
the most famous swords-family (not the most famous individual
swordsman) in Japanese history.
His father, Mitsuyoshi, was principle sword instructor to the
Shogun's family.  (This is not the same surname that Jubei
carries in Ninja Scroll, but my brother is certain that it's
the same individual.)

Apparently Jubei dropped out of sight for a few years in his
youth.  Upon his return, stories circulated of what he'd been
up to during his disappearance, mostly to the effect that
he'd wandered Japan disguised as a ronin, having adventures,
doing good deeds, etc.

Takuwan, surnamed Souhou, was a famous Zen Buddhist monk
who was a penpal of Jubei's father.  At some point, there
were rumors that Takuwan was not just a monk, but also a
ninja and a spy.

Takuwan's writings to Jubei's father have been translated
into English and published as "The Unfettered Mind:  Writings
from the Zen master to the Sword master", translated by
William Wilson and published by Kodansha.