Is it common for Japanese school kids to live alone IRL?
I wouldn't call it common, based on the data I've found, but the situation commonly portrayed in anime, manga and light novels are not unheard of in real life.
According to this study, those aged 15-19 that live alone comprises only about 5% of the population. It's worth nothing that the graph peaks at the age ranges of 20-24 and 80-84. So while there are indeed students living alone in real life, it's not as common as anime, manga or light novels make it to be.
There are also some discussion about this on different sites, some who've had Japanese friends who live alone. Here are some links if you'd like to read about their experiences. Link 1, Link 2, Link 3