Pirates! (I hate those filthy bandits.)

Another potential anti-boarding countermeasure: if you only have one airlock, you could try drafting your own shuttle and docking it there, so that enemy boarders can't dock. Haven't tried this myself though.

Yeah, that don't work, when ever i board a ship i just leave my shuttle on drafted, incase i need to get out "like now! Not in 10 minutes when your done doing circles around the docking port!" :p and if you do that when you say are clearing a pirate ship, if a trade ship is in the sector they will "hack" your ship to move it themselves so they can dock. Kind of annoying

It is fun to half clear a dialect ship and watch a trade ship die trying to finish it for ya, this might be a good spot for communications to come into play, like them "calling" u and asking for help, or permission etc.