That samurai idea would make sense if not for the fact of ninjas in fiction being samurais with masks, like Leonardo from the Teenage Mutant Ninja Turtles, who follows the code of Bushido.
I cannot deny there are some fictional universes that mark the difference, but the Joeverse isn't one of these: remember that Bushido, a member of Ninja Force, had a samurai armor.
Now, if we see the Battle-verse as totally independent of any other Joeverse,

could be not a ninja, since

is the only character identified as such, and bacts much moreninja-like than other versions.

isn't a ninja either in the independent Battleverse, he just keeps his original Commando function with no reference to martial arts.
In the general Joeverse, any masked character who knows martial arts is defined as ninja, so the thing really depends on the Battleverse independence in the eyes of each collector and/or reader.
PD: We should thransfer all these posts to
http://bloodforthebaron.com/phpBB3/view ... f=5&t=9526 and delete this thread to avoid redundance.