That has already been implemented in at least the ircu server software, which Undernet and QuakeNet use. It is called WHOX and also appears in the 005 numeric as such, if supported. For details see
here. This extension to the /who command allows you to specify various options, among which a client-defined query identifier.
That said, I'm sure NNS keeps track of which /who queries it made (and which replies to subsequently block) fully at the client side, because mIRC is currently unable to use the WHOX replies to update the IAL (relevant thread
here).