Yes and no. All reputation gained will be deducted, and all reputation lost will be restored. And as Shadow Wizard correctly noted, there is a special clause for questions older than 60 days: If the question had a score of 3 or more, and is deleted after 60 days or more the reputation gained is not deducted.
You won't suffer a penalty for deletion, but it could (but not often*) count against you for the question ban, but occasional deletion when other posts are of high quality will not result in any negative effect.
* Thanks to Servy, we've learned that there are some exceptions:
With a handful of exceptions, deleted posts either do not contribute to the ban or are unlikely to be salvageable by the author. The biggest exception is authors who delete their questions immediately upon receiving an answer - and they're already warned about this when they go to delete.