TL;DR "sudo apt install thin-provisioning-tools" fixes it.

Adding debugging steps here for posterity.

ubuntu@15-89:~$ cat /etc/docker/daemon.json 
{
  "storage-driver": "devicemapper",
  "storage-opts": [
    "dm.thinpooldev=/dev/mapper/docker--storage-thinpool",
    "dm.use_deferred_removal=true",
    "dm.use_deferred_deletion=true"
  ]
}


After reboot:

ubuntu@15-89:~$ docker info
Cannot connect to the Docker daemon. Is the docker daemon running on this host?

/var/log/syslog:
Jun 20 20:42:11 15-89 dockerd[1542]: time="2017-06-20T20:42:11.938899425Z" 
level=fatal msg="Error starting daemon: error initializing graphdriver: 
devicemapper: Non existing device docker--storage-thinpool"

root@15-89:~# ll /dev/mapper/
total 0
drwxr-xr-x  2 root root      60 Jun 20 20:41 ./
drwxr-xr-x 19 root root    3760 Jun 20 20:41 ../
crw-------  1 root root 10, 236 Jun 20 20:41 control


But lvs shows it:
root@15-89:~# lvs
  LV       VG             Attr       LSize  Pool Origin Data%  Meta%  Move Log 
Cpy%Sync Convert
  thinpool docker-storage twi---t--- 38.00g                                     
               


vgchange -a y didn't work, complaining that a tool called thin_check wasn't 
available. This tool comes with thin-provisioning-tools.

I then installed thin-provisioning-tools and rebooted one more time. Now
docker runs fine.

What's left to check here is if perhaps thin-provisioning-tools should
be a strong or weak dependency of docker.io, like a Recommends or
Suggests.

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https://bugs.launchpad.net/bugs/1657646

Title:
  Missing thin-provisioning-tools prevent VG from being activated

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