Out of curiosity, why wouldn't a hostile power also put a transponder on their drone (maybe one even replaying a nearby plane's code)? Surely that could help it blend in and avoid defenses
More importantly, it's not uncommon when crossing Air Route Traffic Control Centers (ARTCC) regions (eg. from Washington Center, to NY Center) for controllers to instruct pilots to change Squawk codes. Same applies when crossing from one country's airspace to another.
One of these drones, without a bunch of extra avionics would be unable to change transponder codes in flight, and talk with controllers via relay, that would probably double the cost of the drone, or at least significantly increase it.
So even doing something creative, like spoofing the transponder Squawk code, from another aircraft, probably wouldn't help.
Also, with Mode-C, and Mode-S transponders, the later used with ADS-B, which feeds all the flight tracking websites, the transponder transmits altitude.
A SAM operator will figure out somewhat quickly if an airliner is supposed to be at 10,000ft and 250mph but isn't according to primary radar tracking, but much lower and slower, that it's spoofing it's transponder.