Yhyjyk

Should such a contingency become necessary, mission control centers have the ability to contact (e.g. by telephone) civilian or military air traffic control centers, even those located in other countries. Direct communication (i.e. not involving mission control) between the spacecraft and military air traffic control also sounds plausible, given that the military is often involved in spacecraft landings and recovery.

Has any spacecraft ever had the ability to communicate directly with civilian air traffic control?

If the question is that if spacecraft independently initiate communications with random civilian ATC unit, the answer seems to be no.

Civilian ATC units operate on VHF frequencies (118-136MHz) with AM modulation. Besides that, spacecraft should be able to tune in any frequency within the range that an ATC unit is using. Or they could use universal emergency frequency 121.5 MHz.

Space Shuttle, which most likely would benefit from such a possibility, did not carry VHF radios at all.

As for other spacecraft, Apollos used VHF only to communicate between LM and CM and EVA astronauts, and that happened on fixed frequencies.

Gemini used HF and UHF radios for comms, again on fixed frequencies. Similarly Mercury used HF and UHF frequencies.

The closest match seems to be Soyuz, which operates VHF radio in fixed frequency 121.75 for voice comms. So basically, any ATC unit or aircraft could tune in to communicate with overhead Soyuz capsule. I remember that Scott Kelly mentioned in his book that they sometimes picked an ATIS broadcast when overflying an airport that happened to use the same frequency. VHF comms requires “line of sight” so spacecraft on low earth orbit will pass over a station fairly quickly.

I’d speculate that accidental interference by air traffic with communications between spacecraft and mission control is major reason why VHF is not used in space comms. And to carry “backup” VHF equipment just to communicate with untrained, unexpecting ATC unit would service no purpose and would shave precious kilos from the payload.

Yes in the case of the space shuttle.

I recall in shuttle ascent abort training, when the crew was executing an East Coast Abort Landing to an airbase / airport on the East Coast, the commander would communicate with the tower on "guard" as they were approaching the site.

These airports included civilian airports such as Gander, Atlantic City, etc. Clearly some means of communicating with the civilian tower in this situation was necessary.

This line from the Audio/UHF Training Manual (not online) states

UHF guard (243.0 MHz) is available at most U.S. landing fields, and is
used by the crew for East Coast Abort Landings (ECALs).

You can see the reference in the checklist to select UHF transmit/receive. Presumably the frequency was set up prelaunch so they didn't have to mess with changing it during this exciting time. The Training Manual explains

Selecting G T/R on the UHF MODE switch enables transmit and receive on
the GUARD channel frequency in the SIMPLEX mode. All other frequencies
are disabled.

(Ascent Checklist, from the JSC FDF Page)