Maybe it's a difference between those people's standing. Generally the ninja we see everyday are pretty much employees of their villages, doing whatever they are contracted to do. Thus, they have a practical uniform (the vest). These filler characters probably aren't even ninja in that sense. They could be some group of characters with ninja skills but if they are working for themselves, for their own ends and not serving any master, then they wouldn't technically be ninja. In such a case using another form of a garb like a kimono (if they are from such a stock) could be well justified. Although everybody with any skills in Naruto is called a ninja, but I'm not exactly talking about that.