Blocking a mineral or energy deposit when you aren't going to use the habitat for reactor or mining districts is a waste of orbital deposit resources, but even if the AI could build habitats without a deposit it's not capable of planning colony design ahead of time like that. Gestalt empires will waste energy deposits this way even though they already get reactor districts on every habitat automatically.
Primarily this hits technologically enlightened empires though, since they're generally stuck as single-system protectorates, although sometimes poorly-placed federation start empires will run into it as well.