Run gpg --debug ipc --card-status to quickly see the communication with the scdaemon.

$ gpg --version
gpg (GnuPG) 2.3.1
libgcrypt 1.9.3
$ gpg --debug ipc --card-status
gpg: reading options from '/Users/user/.gnupg/gpg.conf'
gpg: reading options from '[cmdline]'
gpg: enabled debug flags: ipc
gpg: DBG: chan_3 <- OK Pleased to meet you, process 15218
gpg: DBG: connection to the gpg-agent established
gpg: DBG: chan_3 -> RESET
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION ttyname=/dev/ttys007
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION ttytype=xterm-256color
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION lc-ctype=en_US.UTF-8
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION lc-messages=en_US.UTF-8
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> GETINFO version
gpg: DBG: chan_3 <- D 2.3.1
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION allow-pinentry-notify
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> OPTION agent-awareness=2.1.0
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> SCD GETINFO version
gpg: DBG: chan_3 <- D 2.3.1
gpg: DBG: chan_3 <- OK
gpg: DBG: chan_3 -> SCD SERIALNO
gpg: DBG: chan_3 <- ERR 100696144 Operation not supported by device <SCD>
gpg: selecting card failed: Operation not supported by device
gpg: OpenPGP card not available: Operation not supported by device
gpg: secmem usage: 0/32768 bytes in 0 blocks

Before downgrading to GnuPG 2.2.27, I created the file ~/.gnupg/scdaemon.conf with a content of reader-port Yubico Yubikey according to this article. The file didn't solve the problem but I haven't removed it yet. Let me know if I shall remove it again.

Also let me know if there are any daemons I have to kill/restart when switching between GnuPG versions by changing the $PATH. Whenever I have problems with my YubiKey, I run gpgconf --kill gpg-agent, which I also executed when I switched from version 2.2.27 back to 2.3.1 but I have no idea whether this is required or sufficient.

If it is built with LIBUSB enabled, please try adding the following to your scdaemon.conf:

disable-ccid

If it works and the distribution doesn't offer appropriate USB configuration, I think that it's good for the distribution to use --disable-ccid-driver for building GnuPG.

Sorry for your inconvenience, this is breaking change in GnuPG 2.3.
Please also see: T5409: scdaemon: 'Operation not supported by device' error under macOS after upgrading to 2.3.1

That would required that we also add an option --enable-ccid-driver - better tell the macOS folks to put diable-ccid-driver into /etc/gnupg/scdaemon.conf

Please read also the report T5442 which is basically the same.

So, has this issue been solved?

Please excuse my late reply. I was busy with other things over the last few weeks.

Yes, putting disable-ccid into ~/.gnupg/scdaemon.conf works for me with GnuPG 2.3.1 under macOS Catalina (10.15).

I still don't understand what the problem is/was, so I cannot judge whether it's better to recommend this manual configuration for Mac users or to disable CCID by default on macOS.

In T5415#146808, @KasparEtter wrote:

Please excuse my late reply. I was busy with other things over the last few weeks.

Yes, putting disable-ccid into ~/.gnupg/scdaemon.conf works for me with GnuPG 2.3.1 under macOS Catalina (10.15).

I still don't understand what the problem is/was, so I cannot judge whether it's better to recommend this manual configuration for Mac users or to disable CCID by default on macOS.

I need CCID to work, disabling this feature is not an option for me (T5442).

At the moment I just downgraded to 2.2, waiting for a fix :-(