A secure cipher is indistinguishable from random data, you can't infer what software is on either end just by eavesdropping.

In practice you can infer a lot. The payload of a TLS stream is formally indistinguishable from random data, but you can still tell on the wire that it's TLS. There aren't a lot of widely-used TLS implementations. It's been a while since I looked at the specifics, but I bet there's a lot of more specific signature data in the plain-text parts of the protocol like supported ciphers. You can make some good guesses from the metadata.

In the case of a physical interception, you can probably infer more. If you, after reading this article, spot an enemy drone that doesn't have any obvious emissions, then, well, there might only be one option for the software running on that drone, namely The Software that your enemy uses on their drones.

Anyway, it's not clear to me from the article whether the source object from the signal will necessarily be invisible. I think every transmitter still at least looks like a point source of blackbody radiation. The signal may not be detectable from thermal background radiation, but if the background itself is coming from a big obvious drone, well, you know it "exists nearby".

But once you've located the device, you can use a number of electronic warfare approaches to crack into it, not necessarily through its main radio interface. For instance, electromagnetic interference, heating, etc, all can inject a subtle hardware failure that the software is not ready to handle.