I can reproduce the bug in 16.04 but it seems to be fixed in 18.04:

$ echo '' | bluetoothctl
No agent is registered
$

$ bluetoothctl < /dev/null
[bluetooth]# quitt to bluetoothd...
No agent is registered
$

I'm going to declare this fix released and nominate 17.10 for a fix
(whatever the fix would be).

** Changed in: bluez (Ubuntu)
       Status: Confirmed => Fix Released

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https://bugs.launchpad.net/bugs/1565940

Title:
  bluetoothctl systematically hangs when there is no bluetooth hardware

Status in bluez package in Ubuntu:
  Fix Released

Bug description:
  On a machine WITH bluetooth hardware, the 'bluetoothctl' command works 
correctly.
  For example, the command 'bluetoothctl < /dev/null' terminates correctly.

  On a machine WITHOUT bluetooth hardware, the 'bluetoothctl' command 
systematically hangs.
  Even the command 'bluetoothctl < /dev/null' systematically hangs.

  $ bluetoothctl &
  [1] 6208

  $ ps -l $!
  F S   UID   PID  PPID  C PRI  NI ADDR SZ WCHAN  TTY        TIME CMD
  0 T  1001  6208  2525  0  80   0 -  9578 signal pts/1      0:00 bluetoothctl

  [1]+  Stopped                 bluetoothctl

  ProblemType: Bug
  DistroRelease: Ubuntu 15.10
  Package: bluez 5.35-0ubuntu2
  ProcVersionSignature: Ubuntu 4.2.0-34.39-generic 4.2.8-ckt4
  Uname: Linux 4.2.0-34-generic x86_64
  ApportVersion: 2.19.1-0ubuntu5
  Architecture: amd64
  CurrentDesktop: X-Cinnamon
  Date: Mon Apr  4 20:09:39 2016
  InstallationDate: Installed on 2015-07-20 (259 days ago)
  InstallationMedia: Ubuntu-GNOME 15.04 "Vivid Vervet" - Release amd64 
(20150422)
  InterestingModules: bluetooth
  MachineType: To be filled by O.E.M. To be filled by O.E.M.
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.2.0-34-generic.efi.signed 
root=UUID=0d11df61-c758-41b1-9ec3-8310bf038b07 ro quiet splash vt.handoff=7
  SourcePackage: bluez
  UdevLog: Error: [Errno 2] No such file or directory: '/var/log/udev'
  UpgradeStatus: Upgraded to wily on 2015-10-22 (165 days ago)
  dmi.bios.date: 06/26/2015
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 2603
  dmi.board.asset.tag: To be filled by O.E.M.
  dmi.board.name: M5A97 R2.0
  dmi.board.vendor: ASUSTeK COMPUTER INC.
  dmi.board.version: Rev 1.xx
  dmi.chassis.asset.tag: To Be Filled By O.E.M.
  dmi.chassis.type: 3
  dmi.chassis.vendor: To Be Filled By O.E.M.
  dmi.chassis.version: To Be Filled By O.E.M.
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr2603:bd06/26/2015:svnTobefilledbyO.E.M.:pnTobefilledbyO.E.M.:pvrTobefilledbyO.E.M.:rvnASUSTeKCOMPUTERINC.:rnM5A97R2.0:rvrRev1.xx:cvnToBeFilledByO.E.M.:ct3:cvrToBeFilledByO.E.M.:
  dmi.product.name: To be filled by O.E.M.
  dmi.product.version: To be filled by O.E.M.
  dmi.sys.vendor: To be filled by O.E.M.
  hciconfig:
   
  rfkill:
   
  syslog:
   avril 03 15:10:45 urbah-sirius systemd[1]: Starting Automatic USB/Bluetooth 
printer setup (-devices-pci0000:00-0000:00:12.2-usb5-5\x2d5)...
   avril 03 15:10:45 urbah-sirius NetworkManager[986]: <info>  Loaded device 
plugin: NMBluezManager 
(/usr/lib/x86_64-linux-gnu/NetworkManager/libnm-device-plugin-bluetooth.so)
   avril 03 15:10:50 urbah-sirius systemd[1]: Started Automatic USB/Bluetooth 
printer setup (-devices-pci0000:00-0000:00:12.2-usb5-5\x2d5).

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