Steps to reproduce:

1) Download attached project 'TestAnimationProject.zip' and open in Unity.
2) Press Play and check Profiler.
Note: you should see 'Animation.Update' Calls. (Objects been disabled by script).(see attached image 'disabledAll.png').
3) Stop Play mode.
4) Select all 'GameObject xx' (should be around 1000) in Hierarchy. Disable all objects through Inspector.
5) Press Play and you should note that Animation.Update wasn't even called.

Expected result: If game object is disabled, Animation.Update should not being called.

Reproduced with: 5.2.4f1, 5.3.6p4, 5.4.0p4, 5.5.0b2