Contrary to popular belief, Kaito did in fact comb his hair. Quite often, actually. Several time a day. And he was always very careful to clean up any stray hairs that may have dropped. Kaito had very good personal grooming habits in general; he showered twice a day (morning and night), scrubbed and exfoliated. There was a damned good reason he never had pimples. And if those habits had improved somewhat of late, nobody was complaining (least of all his mom).
His own continual lack of skin blemishes also gave him the perfect opportunity to rib Hakuba, when the other came to school one day with a great, fat zit on his nose. Kaito had noticed with some personal amusement that Hakuba was scrubbing his hands and face far more frequently after that.
Most teenage boys – even the more "sophisticated" (as proven by Hakuba) among them – had less than exemplary hygiene. They didn't think they had any reason to have good habits. Unlike them, Kaito did have a reason. A very good reason.
The way modern forensic science was progressing, there was no way he could afford to let a single hair, or a bit of dead skin, or a broken nail fall where he couldn't control it. Hairspray (even on the skin) and gloves helped some, but exceeding attention to detail in grooming was far more important. Really, he sometimes thought that his opponents didn't give him nearly enough credit; avoiding forensics these days was a lot harder than it had been in his father's day, and he had to worry about it constantly.
Not that he would ever – or could ever – admit the reason for his constant cleanliness. And as messy as he acted, he didn't think that anyone except Hakuba and Akako had noticed (his mom didn't count.). Between the two of them, Kaito was far more worried about Hakuba; Akako wasn't and enemy, or even an opponent these days, really. And although Kid had never left anything for the forensics teams to find at a heist (and oh, how they combed the sites these days), Hakuba had probably already made the connection. He just couldn't – as usual – prove anything. Kaito intended to keep it that way.
Most criminals got caught because they were careless. In spite of all appearances, Kaito was anything but careless.