That page talks about malicious relays in the sense that they spoil traffic either through incompetence or malfeasance.

What I am thinking about is the hypothetical case that 3000 of the 6000 active relays today had been started and operated by Eve over the last few years according to Tor guidelines and without any external sign that the nodes were centrally controlled.

If that were true it would be hard for a user to detect, and it seems to me that Eve would be able to reasonably easily break the privacy protection of Tor.