When a trunksd process is stopped (using 'initctl stop trunksd' or by sending a signal) it doesn't go through proper shutdown procedure. Attempting to do anything in hooks like DBusServiceDaemon::OnShutdown() fails - they are simply not called.
A single line "init: trunksd main process (NNN) killed by TERM signal" is added to the logs.

Analysis:

Trunks daemon starts a DBusServiceDaemon instance (for handling D-Bus requests), which registers SIGINT/SIHTERM/SIGHUP signal handlers (in brillo::Daemon::OnInit()) to properly handle shutdowns (and restarts).

However, trunks daemon also starts a background thread for BackgroundCommandTransceiver. This thread doesn't register any signal handlers. As a result, when SIGTERM is received, the process is terminated before DBusServiceDaemon can properly shutdown D-Bus.

Here is what happens on receiving SIGINT when both threads are running (strace -f trunksd):

========
[Main D-Bus thread detects the signal and starts processing it]
[pid   822] <... epoll_wait resumed> [{EPOLLIN, {u32=10, u64=10}}], 32, -1) = 1

[The background thread is also woken by the signal]
[pid   823] <... futex resumed> )       = ? ERESTARTSYS (To be restarted if SA_RESTART is set)

[The main D-Bus thread unregisters the signal handler and moves on to doing other cleanup]
[pid   822] epoll_ctl(3, EPOLL_CTL_DEL, 10, 0x7ffcef72a790) = 0
[pid   822] write(7, "\0", 1)           = 1

[But the background thread doesn't process SIGINT and the process decides to die]
[pid   823] --- SIGINT {si_signo=SIGINT, si_code=SI_USER, si_pid=1045, si_uid=0} ---
[pid   823] +++ killed by SIGINT +++
+++ killed by SIGINT +++
========

If commenting out the background thread, the main dbus thread shuts down correctly and calls OnShutdown():

========
[The main D-Bus thread wakes up on SIGINT]
epoll_wait(3, [{EPOLLIN, {u32=6, u64=6}}], 32, 0) = 1
read(6, "\0", 1)                        = 1
write(7, "\0", 1)                       = 1

[Prints OnShutdown debug message]
sendto(9, "<11>Jan 30 20:08:09 trunksd: OnS"..., 40, MSG_NOSIGNAL, NULL, 0) = 40

[...skipped...]
[Unregisters on D-Bus]
sendmsg(11, {msg_name=NULL, msg_namelen=0, msg_iov=[{iov_base="l\1\0\1\30\0\0\0\3\0\0\0\177\0\0\0\1\1o\0\25\0\0\0/org/fre"..., iov_len=144}, {iov_base="\23\0\0\0org.chromium.Trunks\0", iov_len=24}], msg_iovlen=2, msg_controllen=0, msg_flags=0}, MSG_NOSIGNAL) = 168

[...skipped...]
[Unregisters the signal handlers]
epoll_ctl(3, EPOLL_CTL_DEL, 10, 0x7ffd75d4e290) = 0
close(10)                               = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0

[...skipped...]
[Closes /dev/tpm0]

epoll_ctl(3, EPOLL_CTL_DEL, 6, 0x7ffd75d4db60) = 0

[...skipped...]
[Exits normally]
exit_group(0)                           = ?
+++ exited with 0 +++
========