I think we still need to understand the terms we're using here.
Samurai was a hereditary title awarded by the leaders of the government.
That means if you were a samurai, it's because someone awarded it to you, or you were born to samurai parents.
As a note, three out of five of the martial arts you mentioned are modern, and were not practiced they're presented here.
Ninja wasn't even a term used at the time. It's a modern term for a feudal spy.
It's not some mysterious hidden school of people with their own fighting styles. They were just spies. Most of them trained in conventional samurai schools, and took to battle the same way your conventional samurai did. Now there were special ninpo schools, but they taught very minimal fighting. The little bit that they did teach was escape and specialty tools. The rest was things like impersonation, silent movement, breaking and entering. It's assumed that the bulk of one's fighting ability would come from a conventional school, especially as far as the battlefield goes. Also, the kunai was an unsharpened trowel, generally about the size of a small man's forearm. Nothing small, or knifelike about it.
Taijutsu is just a name for body movement, specifically in fighting. Many samurai schools use the term as well. Despite what Naruto says, it's not just a ninja thing.
Now, many of the people born into samurai families or who were awarded the title samurai did primarily spy work.
It's also obvious that, while samurai is seen as military title, not everyone born with it or awarded it was anything special as far as fighting goes. A great deal of them were primarily politicians.
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As stated in the last paragraph, there might have been schools, established by landlords or even the emperor to do the dirty work, which makes them samurai in a way. However, they do NOT conform to the classic title of Samurai
No, sorry, a great deal of martial schools that still exist contain an espionage component. It wasn't this hidden exception that the evil landlords made up.
Look at Tenshin Shoden Katori Shinto ryu to start.
Less anime, more study.