I don't know why you think it's low-key hilarious. There's no explicit law forbidding bullying. Assault, slander, libel, and verbal abuse (to a degree) are covered, but you'd have to make the case that the bullying escalated to the extent of one of those accusations. Yes, we were solidly in the realm of verbal abuse here, but it can be harder to make a solid case without hard evidence such as verbal recordings or writings. (The assumption being that, with the exception of the desk itself, everything else was taken down and trashed and would be unavailable as evidence.) There's a burden of proof that's required before punishment can be meted out, and that's hard to do when it's just spoken and unrecorded.
However, property damage is also covered by law, and it's much harder (if not impossible) to cover up as evidence. So in effect, the teacher is confronting the kids on the charge where they'd be the most legally vulnerable. He's attacking from the direction that would incriminate the worst of the offenders, and definitely startle the implicit bystanders and verbal bullies. The teacher's first salvo, in effect, is stating that this can't be covered up, and we will eventually corner you and prosecute you.
Yes, the not-fully-cleaned writing on the desk is also evidence, but that just scales back the severity, especially in light of the teacher's other statements. Trash talking someone else is just one person's word against another, but defacing public property puts the offender against everyone who contributed to said property. In this case, the public itself. And in Japan, where it's culturally important to act in the betterment of the community over oneself, that's the far greater crime.
