The Ender Dragon will not spawn in a fresh, un-entered End dimension if the island is loaded by an Ender Pearl. It will only spawn if a player enters the End.

Reproduce:
1) Delete the DIM1 folder in the world save to restart the End completely.
2)) In Overworld, throw Ender Pearl into End Portal and teleport it to 0, 128, 0 repeatedly, consequentially loading the 0, 0 chunk in the End consistently.
3) Run command to /kill the dragon and see that it says no entity exists. Once a player enters the End Portal, the Ender Dragon will appear. (see the two latest screenshots)

If a dragon has been spawned already, it is possible for commands to return information on it when it is loaded by an Ender Pearl with no players in the End (see earliest screenshot)