There's no one way to handle this. Clarification can mean so many different things, best handled by different action. As a general note, the cost to leaving valid clarification requests up is pretty minimal.
The key idea when handling questions (or answers for that matter) from deleted users, is the utility to future readers. This concern is always applicable, but when the post owner is still active, it's usually better to take it with them.
So, when encountering old clarifications (and the user is deleted/no longer active) ask yourself, would this make the post better? Good here means clear, focused, and useful. If the matter being clarified is minor, user/person specific, or tangential it can probably just go away. Consider flagging as NLN or using a custom flag giving that rationale.
If the the clarification request is more substantial (but not such that question was closed), consider fixing the question yourself. The bounds editing an "abandoned" post is a bit looser, but the goals here should be to make the question as much as possible ask for the answers it already has.† There's no one way to handle this, consider consulting other users (eg. in chat) about the specific case, or just leaving it alone, it's probably fine.
†– we actually do fix questions to match their answers on occasion, though usually that's to help a new(er) users with a question that's too broad/unclear but which got a helpful answer before it got closed.