Are you referring to this?
https://itch.io/docs/creators/quality-guidelines#avoid-obtrusive-advertisements-...
That is quality guidelines. Not tos. If people complain about your game, it might get removed from index, if staff agrees.
In other words, obtrusive ads are not forbidden. What is forbidden, is "adware". And from context it can be assumed that they talk about the malicious kind of adware and not the technical definition of games that get revenue by showing ads, like so many mobile apps do.