It may be a good idea to have a patrol option when giving commands to ships.
A ship in patrol would fly around a predefined path and attack all enemy vessels that come into range.
This would be beneficial especially when protecting one's trade routs.
Also one could imagine having different patrol options:
auto-engage all
engage only military targets
engage only weaker targets
just scout
The last two would pause the patrolling ship and request the player's attention when some targets come into range