Its only really the tail aircraft symbols that cause an issue.
The ground unit insignia such as the Afrika Korps one with the palm tree and hakenkreuz are too small to really be noticeable in a game.
Air Identification flags on tanks came later in the war. Also whilst many units did just use the NSDAP Flag or sometimes the Third Reich Battle Ensign the official Balkenkreuz Air Identification Flag shown below was also common and its historically accurate to use that on ground vehicles.
The Balkenkreuz Air Identification Flag was never flown as a flag but is commonly used in this role as a substitute for the NSDAP Flag by WWII recreation groups.