Scapa Flow's air defences answered a real German threat

Did Germany consider attacking Scapa Flow from the air as well as by submarine?

Yes. The possibility of air attack explains the base's heavy defences, and control of Norway materially affected the threat geometry.

Scapa Flow was not defended only against submarines and surface intrusion. German aircraft also presented a credible route of attack against the fleet anchorage. That danger justified substantial air-defence measures around the base. Norway's status mattered because northern airfields and approaches could move German aircraft closer to the anchorage and change the warning and interception problem.