From what I remember there isn't any written evidence for the ninja-to or the traditional black suit. They were disguised as civilians or wore armor if they expected fighting (though hard evidence for armor is scarce too).
Black suit or specialized weapons were a product of theater, but actual identity and deeds are murky precisely because of what they do. A ninja you know anything about is a ninja that screwed up.
Reasoning from the practical level(rather than historical), ninja are as likely to work for a specific lord as for general mercenaries. In the latter case, trust is a serious issue, your personal spies and assassins can be trusted more to do their job rather than sell you out. While they perform dishonorable jobs, I rather doubt political leaders give much of a crap as long as they can keep it unassociated with them. Heck, practically speaking, if you were to have an actual ninja
tradition you more or less need to tie yourself to a certain line of leaders for support, and some level of protection against being rooted out, as mercenary ninjas would be the sort of danger you'd want to be rid of if you aren't in charge of them.
Gear wise, disguised, concealed or improvised weapons and armor seems to be par for the course. The key thing is getting there undetected and then offing your target. This gives a wide variety of approaches, most common work tools can be weaponized with a little work, while poison and the like do a lot without risking a straight fight with a professional soldier. Pretty unlikely to have actual swords though, swords are costly to have and to craft, difficult to conceal and practically impossible to explain away. So you get shuriken and needles(concealable and ranged, so you can do a poisoned hit and run), you get kunai and other sharpened farm tools, you get chain weapons wrapped around the body, you get weighted sleeves and other enhanced clothing, etc. Of course, unarmed combat as well, as the final resort.
