Do we have any evidence whatsoever that black boxes still work? I mean actual, concrete evidence of their use, not "They're different from HPGs so they must still be useful" speculation.
Yes.
From Ghost War:
Mason and Janella recieve a message that was routed to them by way of some sort of republic black box network.
Mason was also able to get word off-planet through some manner of automated system that was able to get data off-planet from a coffee shop's register system. They don't SAY its black-box based, but there really arent that many candidates, technology wise, and the HPG network is down.
From Daughter of the Dragon:
it does indicate that the combine has lost some to time, they still have black boxes, and they are mentioned as being old but functional
They're mentioned "working like a charm"
2: They're inherently unsecure. Every Black Box that you control or don't control that is within range will pick up the signal. They not only broadcast omnidirectionally, their limited transmission capability means only the most basic of encryption can be used. You won't broadcast anything via Black Box that you wouldn't want to broadcast directly to enemy HQ.
The combine-controlled black boxes that they used to eavesdrop, were mentioned as being directionally shielded, to avoid being eavesdropped upon themselves. You can focus them.
As for the matter of being overheard, you could run them like a
Numbers Station if you believed that they would infact be overheard. Units get a One-Time pad and there's no worry of the wrong person decoding the orders because its a one way thing. If you don't have that one time pad to decode it, its gibberish to you.