a Ka'Tan has LOADS of other weapon systems in its other fire arcs anyway so its not really an issue! A Ka'Tan has in fact got SIX weapon systems, its beam, its emine, and four seperate pulse cannons.
In any case as far as Im aware the restriction for close blast doors applies to the ships actual weapon systems as listed not what it currently has (if it loses guns due to crits, one shot or is reloading a slow loading weapon it can still fire one weapon as long as it originally had more than 1).