Well, if you look in museums and display collections, you will never find a ninjato. There are thousands of katana, wakizashi and tanto, but no ninjato. You would think there would be a least a few antique ones floating around.
Or maybe they were so secret that they were all melted down???

Assasins need to blend in, so they also didn't wear special all-black uniforms. Now did they wear darker clothing to attack at night? Probably.
Now there WERE some variations of the katana, some were fairly straight, others more curved, and also the lengths, espcially of the oldest ones were not standard. Also with as much work as it took to make a blade, if one broke near the tip it may have been reworked into a shorter blade. So it IS possible that someone found an older, somewhat straighter, shorter version with plain fittings and thought it was used by ninja. Or was told by some less-than-honest sword/antique dealer that it was.