Are you playing with fog of war? If yes, the FoW combined with putting your units in difficult terrain - forest, towns - will make them harder to find. Air bases are easier to find because any time an air unit from that base is active it might reveal some information about the base (radar, or following the enemy air units back to their base if there has been a2a combat). I would think that a recon plane flying over a base would be able to get pretty good intel on what types of aircraft are present there, though maybe not exact numbers. The size and number of hardstands, hangers, auxiliary buildings, etc. would give you at least a good idea of bombers/fighters single-engine/multi-engine and a rough idea of how many.
It is kind of odd in general that good aerial recon will give you information about the specific unit, but remember military aircraft often have distinguishing marks on them indicating what squadron/regiment they belong to. Also, the system doesn't distinguish between detection levels gained by adjacency (where unit ID would certainly be available from casualties or POW's) and aerial recon. Also, there is some electronic intelligence going on, intercepting communications and the like, and in-person recon by partisans and special forces teams supplementing information gained by air recon overflights. I have often felt that there should be some random revelation of units in the rear, especially in enemy territory, to account for partisan/spec forces operations.