I seem to notice that there is no request to remove emulation of the systems, but only the links to the ROMs
Correct, and such a request for the emulators won't be possible at all: it's definitely not forbidden to write an emulator for whatever program/system you want, as long as you don't use any original code.
And so removing the Vancouver emulation from the Mess-SVN a few days ago is absolutely incomprehensible for me!
Indeed. I see no threat against the actual emulation there, nor is there any grounds for one. They have every right to request the site don't host their roms however.