On connecting to a modded server the player *should* be prompted to reconfigure their client to a server-compatible state (ie. download, enable or disable mods.)
Their client should then automatically restart (if necessary) and reconnected to the server in question.
This client reconfiguration mechanism could prompt players to subscribe to the needed to mods in the Steam Workshop or smaller mods could be downloaded and installed directly from the server, like mission files. Server admins could control which mods can be downloaded via settings in the server.cfg file.
Other client-server games have worked this way since the late 1990s.