It's a coincidence based on a stupid pun. Batman's was tolerable because Harley was a great original idea from Bruce Timm (it eventually spilled into the regular comics, even!)...Chrono Cross', I suppose, is tolerable because we don't have a name for that Moon Goddess word or w/e, I guess...
But yeah, they dress like clowns and have names based on the fact that they're dressed like clowns...go figure...