A ship without transponder activated can't be confirmed to be anyone without accurate sensor reading. It could be potentially abused to strike at a rival faction without revealing yourself, thus leaving the culprit of the attack to remain unconfirmed. You'd have to be really, really careful about it thought, because if the ship used in the attack is identified and then seen flying your colours, the gig is up.
So like old school privateers.
In that particular instance, yes. In a more real world scenario, transponders are used, particularly in aviation, for traffic control and international controls. Most nations have air defense zones, and in times of war, or in particularly sensitive areas, transponders are a necessity to not getting shot at.
As a poster above mentioned it, its kind of a politeness thing. "Hi, its me your boring commercial hauler, im supposed to be here, and my flight plan is filed" kind of thing. Something that can be easily checked against.
As for "false flagging" as mentioned by the previous poster, in the privateer or secret strike role, its a high tech spoofing of a transponder to make you show as something you are not, or to black out your force so as to not give away your identity.
That would only work once, and only for ships that had not been encountered before. By Steve's previously established EW logic, most ships that are scanned by sensors are recorded and logged. So, much like modern submarines, that log can be reviewed to identify a ship, any time it is seen again. That being the case, a false flag strike on another power would only work if those ships were never going to be seen by that power again. Otherwise, they are eventually going to figure it out. That also includes the classes involved.
So, while you could in theory turn of your transponders, attack another power, its only going to work once (ok, maybe a few times) and only if the ships and ship classes used are never used by your empire again. Otherwise, your busted.