Using hook_mail_alter() for pending approval admin does not make any effect
The emails are being sent because in admin/config/people/accounts the option Visitors, but administrator approval is required is selected for Who can register an account.


  


If you selected Visitors or Administrator only no email would be sent.

In the case you wanted to just avoid emails where sent to the administrators, but still wanted the administrator users to approve accounts, then the implementation of hook_mail_alter() should look for messages whose ID ($message['id']) is equal to user_register_pending_approval_admin_. Also, the example in the documentation of hooks don't show the correct name a hook implemented by a module should have: Always replace hook_ with the short name of the module implementing the hook.