The correct reading of 柳生十兵衛 is yagyuu_juubee, but this site lists it as Yagyuu Juubei .
I checked Japanese Wikipedia and dictionaries, and all of them use juubee.
Also, 十兵衛 is not a personal name but a title, the same kind of title as "Hanbee" in Takenaka Hanbee.
Interestingly, this site lists 竹中半兵衛 as Takenaka_Hanbee, so I am curious about the difference in treatment.
If I were to create a BUR, would it be better to use the alias instead?
I personally think that only Yagyuu Juubei himself, the Yagyuu Juubee from Hyakka Ryouran, and Yagyuu Kyuubei should use an alias, and for all other cases a rename would be sufficient.