I've played Khreathor's map again to see if I could find the remaining secret. Eventually I've given up and noclipped to see where it is, but I couldn't figure out how to activate it, not even with r_fullbright 1.
After a lot of searching
I've finally found it, but that's surely one of the most elusive secrets I've come across in Quake maps. I didn't expect the button to be downsized, so my brain ignored it when looking for buttons.
By the way, I've had the same problem with a secret in Fifth's Q-Deck: one of the secrets was activated by a small button.
It seems that the mind gets used to the usual sizes of buttons in Quake and assumes those as a standard, ignoring everything smaller when looking for buttons.