OS is Tumbleweed.

Each run of "zypper up" leaves one or two processes of gpg-agent running.

Example 1 is when nothing is changed in the repositories, it leaves one
gpg-agent process running in .../zypp-trusted. Example 2 forces a download of
repo-update, this leaves two gpg-agent processes running, one in
.../zypp-trusted and one in .../zypp-general. The directories under
/var/tmp/zypp. are deleted after zypper exits.

>From the gpg-agent manual page, the option --daemon is supposed to keep the
program running, --use-standard-socket has no effect. The right option seems to
be --server so that gpg-agent accepts commands on stdin but exits as soon as
stdin closes.
Also, why is gpg-agent started at all? It is started with a temporary directory
as --homedir, and then queries for the existence of keys within this newly
created directory. 

Example 1:
# killall gpg-agent
# ps l -C gpg-agent
F   UID   PID  PPID PRI  NI    VSZ   RSS WCHAN  STAT TTY        TIME COMMAND
# strace -s200 -feexecve zypper up
execve("/usr/bin/zypper", ["zypper", "up"], 0x7ffcbf82e648 /* 59 vars */) = 0
[pid 30952] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--import", "--homedir",
"/var/tmp/zypp.aU8FU1/zypp-trusted-krZsV9rZ", "--no-default-keyring",
"--quiet", "--no-tty", "--no-greeting", "--no-permission-warning",
"--status-fd", "1", "/var/tmp/zypp.aU8FU1/TmpFile.Uo0CEU"], 0x7f896ae64950 /*
62 vars */) = 0
[pid 30954] execve("/usr/bin/gpg-agent", ["gpg-agent", "--homedir",
"/var/tmp/zypp.aU8FU1/zypp-trusted-krZsV9rZ", "--use-standard-socket",
"--daemon"], 0x7ffe75b26b90 /* 62 vars */) = 0
Loading repository data...
Reading installed packages...

Nothing to do.

<---- here strace waits for gpg-agent to exit, killall gpg-agent from another
terminal is necessary

--- SIGTERM {si_signo=SIGTERM, si_code=SI_USER, si_pid=30959, si_uid=0} ---
+++ exited with 0 +++


Example 2:
# killall gpg-agent
# ps l -C gpg-agent
F   UID   PID  PPID PRI  NI    VSZ   RSS WCHAN  STAT TTY        TIME COMMAND
# rm -r /var/cache/zypp/raw/repo-update/repodata
# strace -s200 -feexecve zypper up
execve("/usr/bin/zypper", ["zypper", "up"], 0x7ffd98d67d48 /* 59 vars */) = 0
[pid 30968] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--import", "--homedir",
"/var/tmp/zypp.ajNXqC/zypp-trusted-kr3Ntfzf", "--no-default-keyring",
"--quiet", "--no-tty", "--no-greeting", "--no-permission-warning",
"--status-fd", "1", "/var/tmp/zypp.ajNXqC/TmpFile.DV3RZv"], 0x7f928f72f950 /*
62 vars */) = 0
[pid 30970] execve("/usr/bin/gpg-agent", ["gpg-agent", "--homedir",
"/var/tmp/zypp.ajNXqC/zypp-trusted-kr3Ntfzf", "--use-standard-socket",
"--daemon"], 0x7fff7bbcf4d0 /* 62 vars */) = 0
[pid 30976] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "-v",
"--no-default-keyring", "--fixed-list-mode", "--with-fingerprint",
"--with-colons", "--homedir", "/var/tmp/zypp.ajNXqC/PublicKey", "--quiet",
"--no-tty", "--no-greeting", "--batch", "--status-fd", "1",
"/var/tmp/TmpFile.Nw0oTp"], 0x7f928f72f950 /* 62 vars */) = 0
[pid 30977] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--import", "--homedir",
"/var/tmp/zypp.ajNXqC/zypp-general-krpJJyHS", "--no-default-keyring",
"--quiet", "--no-tty", "--no-greeting", "--no-permission-warning",
"--status-fd", "1", "/var/tmp/TmpFile.Nw0oTp"], 0x7f928f72f950 /* 62 vars */) =
0
[pid 30979] execve("/usr/bin/gpg-agent", ["gpg-agent", "--homedir",
"/var/tmp/zypp.ajNXqC/zypp-general-krpJJyHS", "--use-standard-socket",
"--daemon"], 0x7ffcbd2c79a0 /* 62 vars */) = 0
[pid 30982] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--homedir",
"/var/tmp/zypp.ajNXqC/fake-keyringrJDqo5", "--no-default-keyring", "--quiet",
"--no-tty", "--no-greeting", "--batch", "--status-fd", "1",
"/var/cache/zypp/raw/repo-updateMgLSnY/repodata/repomd.xml.asc"],
0x7f928f72f950 /* 62 vars */) = 0
[pid 30983] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--list-public-keys",
"--homedir", "/var/tmp/zypp.ajNXqC/zypp-trusted-kr3Ntfzf",
"--no-default-keyring", "--quiet", "--with-colons", "--fixed-list-mode",
"--with-fingerprint", "--with-sig-list", "--no-tty", "--no-greeting",
"--batch", "--status-fd", "1"], 0x7f928f72f950 /* 62 vars */) = 0
[pid 30984] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--list-public-keys",
"--homedir", "/var/tmp/zypp.ajNXqC/zypp-general-krpJJyHS",
"--no-default-keyring", "--quiet", "--with-colons", "--fixed-list-mode",
"--with-fingerprint", "--with-sig-list", "--no-tty", "--no-greeting",
"--batch", "--status-fd", "1"], 0x7f928f72f950 /* 62 vars */) = 0
[pid 30985] execve("/usr/bin/gpg2", ["/usr/bin/gpg2", "--verify", "--homedir",
"/var/tmp/zypp.ajNXqC/zypp-trusted-kr3Ntfzf", "--no-default-keyring",
"--quiet", "--no-tty", "--batch", "--no-greeting", "--status-fd", "1",
"/var/cache/zypp/raw/repo-updateMgLSnY/repodata/repomd.xml.asc",
"/var/cache/zypp/raw/repo-updateMgLSnY/repodata/repomd.xml"], 0x7f928f72f950 /*
62 vars */) = 0
Retrieving repository 'repo-update' metadata
-----------------------------[done]

Nothing to do.

<---- here strace waits for gpg-agent to exit, killall gpg-agent from another
terminal is necessary

[pid 30980] --- SIGTERM {si_signo=SIGTERM, si_code=SI_USER, si_pid=31129,
si_uid=0} ---
[pid 30971] --- SIGTERM {si_signo=SIGTERM, si_code=SI_USER, si_pid=31129,
si_uid=0} ---