An interesting variation or house rule on this would be if airbases could scramble everytime a warship passes by their seazone, on their way to another SZ, either on combat or non-combat movement. Airbases would then be able to block certain naval routes and you'd have to conquer them first before advancing.
Or you could just have them fight one round as they pass if the ships are just passing through, similar to fighter interceptors for SBRs.
That's more balanced than the my original idea: large fleets might still be able to get through, while smaller fleets would risk being sunk.