Does the mod team not understand a joke?

Well it doesn't say it directly, yes, but the PB board is meant to be a heavily serious board where people go to get feedback against bans, hacks, whatever their issues may be. So it should be kind of common sense to not be saying something that is seen as a meme, joke, not serious when replying there.

https://boards.na.leagueoflegends.com/en/c/player-behavior-moderation/OjEUxbwH-player-behavior-rules-update

Most people who come to Player Behavior after a ban or chat restriction are frustrated, angry or upset. It is important that our responses remain positive and come from a genuine desire to help them understand what happened and why. Replies that are overly negative, dismissive or combative are not appropriate and may be removed.

Things like "Ok boomer" can be rather dismissive as is says in there, so that's what that would fit under.

{quoted}

And where do we see those guidelines?

Sukishoo has it right. I would add this, however:

These include (but are not limited to):

Telling people you’re glad they’re banned. ** Low-effort taunts such as the Rammus “ok”.** Saying the community is better off without them.

In this case, we considered "okay, boomer" a low-effort taunt.