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Note that MDS is /not/ necessary for <playership> /manual/ use (though its manual function may require an explicit keybind in <settings>); neither do manual or automatic anti-missile measures require Mosquito missiles to be explicitly selected in <playership> loadout: they simply have to be in the ship's cargo. MDS simply automates the counter-missile launch for both <playership> & any NPC ship
Also note that to conserve your missiles, the MDS will not attempt to destroy all missiles, it determines which missiles to take down based on their destructive power and your current level of shields. If you shields can easily absorb the damage, a Mosquito is not wasted to take it down. Therefore some missiles will hit your ship3, but they shouldn't do much damage to you3