In addition to astrotech beams, let it "time out" after a short time period.
I agree with Lukwan. A tracker probably needs to be an additional block, place-able through shields to become part of the target ship.
Maybe if it's an actual block, it could have a "sticky" effect, so that if it is launched from a rail launcher, it can do some things on impact with the target. (I.e. the tracker entity that is launched actually disappears on impact, and the point of impact has a new tracker block added, so the net result is the hunter entity is down a tracker block and a ship core, while the target entity is plus one tracker block that is transmitting to the hunting faction.
Varying levels of "detectability" on either side would be fun. It probably needs to be a matter of how many scanner antenna to determine range and accuracy of detection. So if the target has only a few antenna blocks, the tracker's nav beacon is bouncing all over the place in a 80-block radius. I imagine if the random bouncing is random enough, a player could simply watch the nav beacon for a while and get a good idea for the "center", where the tracker is actually located. However, this takes time, and would give the enemy time to track them, for whatever use it would be.
It would be worth discussing what would happen to fleet orders or anything else that is affected by the tracker: What happens when the tracker expires, is destroyed, or otherwise turns off in the middle of an operation focused on tracking the target? Is the last absolute position of the tracker stored when it goes off, and fleet (or whatever is tracking the tracker) continues to that spot in the universe, regardless of where the actual target has gone? That would probably be the most logical way to handle it.