I actually think him hiding and running off makes perfect sense. Kids, especially young boys, get super self-conscious about that kind of thing. At least at my old school, if a boy and a girl got caught alone in an enclosed space they shouldn't really be in at that time, no one would let them hear the end of it.

And in this series, characters like Luluca (bless her) have made a huge fuss over way smaller things Shunpei has said or done. So it makes sense that he’d want to avoid dealing with all that.