One moment.
Spoiler
Gameplay > Realism
Ahem.That aside, I think the name "Transponder" makes perfect sense in Starsector. I have no idea what the word actually means in the literal sense, but it's easy enough to get a general idea - it sounds to me like some kind of emitter that produces a signal; in the case of Starsector an identification signal for a fleet.
Also, the argument that "new players won't intuitively know what it does" kinda falls flat when you realise that the whole purpose and function of the Transponder ability is explained, very clearly,
in the campaign tutorial. Sure there are players who somehow manage to miss or actively skip the tutorial, but they're a pretty small minority, and on top of that, usually do so deliberately because they enjoy learning a game by trial and error. (Yes I know there are some terrible people who skip tutorials because they're "boring" and then whine to the Devs and the rest of the community because the game is "too hard" - but let's not talk about them here.)
To go back to my opening quip inside the above Spoiler tab, this is a video game. Not real life. Realism and analogies to reality take the backseat in place of making gameplay understandable and enjoyable for a prolonged period of time - sure, you could change the name to something as slap-in-the-face obvious as "Identification System" because it sounds closer to what's used in the real world, but I honestly think the change in intuitiveness of the name is so minute that it isn't worth it.
Finally, those of us who have been with the game even for a little while are very familiar with the infamous Transponder. Changing its name now would probably confuse more people than it does already.