The fun/scare/uncertainly of not knowing who is a player and who is an NPC would far outweigh the pesky issues (i.e. trying to figure out who to hail, and who to ignore). Half the time I can tell just by the way the ship is being flown. It would make a pirate's life more difficult for sure, and a traders life a little easier as they would have a better chance at skirting under the radar. If they did this, it would be prudent to make NPC ships actually pirateable at the same time (i.e.. they are actually carrying valuable cargo, and you could actually drop a requested amount to try and save their own skins).
But.. it won't happen. Makes too much sense.