I've performed a research and I could find this was already asked in times past:
CQ-1802 - Hide the ability to ask questions globally (or hide global questions) - enforce all questions to belong to a space.
This is still opened, so I'd suggest you to vote and watch the report to get any updates on it.
We had the same Problem. We did hide the central search form and the Questions Links in our theme via css. If we want to use Questions in a space, we can make the Link visible via css in the space administration.
But I have to admit, that this solution is not very good concerning the Overall usability.
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