I see no severe technical reason why Visualforce pages cannot be deleted from Managed Packages while other Metadata can.
What is the rationale behind that and are there plans to allow that?
Since Spring'15 this is possible. See here.
It is possible that a Apex Controller class could reroute the user to a Visualforce Page. If you delete the VF Page than its possible you could break the managed package.
public ApexPages.PageReference routeUserToSetupScreen()
return new ApexPages.PageReference('/apex/SetupDataScreen');
If you did that then the managed package would break functionality. Users would get the 'not found' screen of death. And since it is managed package, you could not go in an fix controller code.
That is one technical reason why. There are probably others.