This issue has the highest priority and will be addressed with the next release.

Beside the Bf 110 and Ju 88, are there other aircraft that need a non-default fuze?

With the current release the only option is to edit the generated mission. After it was generated (when you see the briefing screen) you quit the game. Then you can edit the mission file (located in "mission/IL2DCE/<name of pilot>"). If you continue the campaign the edited file is used. Sorry this is not a very good workaround