Matrix does not "log all chats". There were some IRC channels which had been explicitly configured by their chanops in the past to be "world readable" in Matrix parlance (i.e. opting into being publicly viewable), which meant that they showed up on archive.matrix.org.
It seems this caused concern because archive.matrix.org didn't have UI to explain why a given channel was visible (i.e. "chanop Bob explicitly set this channel to be world-readable on the Matrix bridge on Jan 1 2017") - and so after we got complaints from ircops last weekend we immediately took the service down to double-check and add the UI to spell out what's going on (and give the IRC channels & networks in question a chance to mark themselves as non-world-readable if that's what they want).
As I said, we're trying to be good neighbours, but there's a lot of ill will flying around.
