Wouldn't it be awesome if one of those "looking for a technical co-founder" types would say they were looking for a programmer "who knows how bad they are"?
The dictionary basically defines "ninja" as someone who is skilled in stealthy movement and camouflage. Interpreted by me to mean someone who can sneak in and do the job without being seen.
Given the innate ability to do the job of programming from anywhere, at any time, I am of the opinion that many programmers can meet the description of ninja. I know in my career, I have worked closely with several people whom I have never actually met.
I do think the usage of ninja is silly, myself. But I do understand that it is more descriptive than just telecommuter, which still seems to imply some physical contact with others.