"have hidden" means the keys were hidden in the past, but it also strongly suggests that the keys remain hidden in the present, or that at least for some reason we need to know in the present where "he" might have hidden those keys. It does not refer to a habitual action.

have hidden -- is present perfect. would is a modal verb Present perfect focuses on the result (Keys are hidden) instead of the action of hiding. The meaning is not every day; it's not a habit. The action of hiding is in the past.

The sentence "Where would he have hidden the keys?" is in the past tense and implies a past event. The use of "would have" in this sentence is an example of the conditional perfect tense, which is used to describe a hypothetical or unreal past event. If the sentence were in the present tense, it might be phrased as "Where does he hide the keys?" or "Where is he hiding the keys?" to indicate a current or ongoing action. Alternatively, if you wanted to use the conditional tense to describe a hypothetical future event, you might say something like "Where would he hide the keys if he needed to?" or "Where might he hide the keys in the future?"

Would is used in sens of want and sentence is present perfect.