Well, there are a few reasons I can think of. S&P had a problem with nunchaku. They are dangerous weapons (like swords sai aren't

) that are
easily simulated. In a few countries, and states here in the US, they are nearly illegal.
Also, they are pretty hard to draw in action, much less animate (as someone pointed out to me.)
Mike hasn't always used his nunchucks. In the third episode A Thing About Rats, he uses mankiki gusari (might be spelled wrong, I'm too lazy to check) against the Foot robots.