1. Make a default cube with a hair particle system
2. Edit the hair in particle mode (comb once or twice)
3. Scale down the cube
4. Press "Apply Scale" on the cube
The hair will "grow" proportionately to how much the cube has been scaled down. This means that the "Apply Scale" function doesn't take hair size into account. There is a workaround for this if you disconnect the hair, apply scale, and then reconnect, but this is very unreliable as it often mangles up the combed hair once you reconnect it again on more complex meshes and setups (perhaps not enough float precision for this?). Even with the default cube you can see a slight shift in the hair position once you reconnect it after applying scale.
The tool "apply scale" changes the basic geometry of meshes, which is used by the particle code to define emission.
There's really a difference between Object size and the actual size of its geometry, these are two independent quantities.
What you probably mean is to have code to inversed correct (change) particle settings for this case. I'm not sure if that's even wanted or possible... but I'll ask the particle coder for final verdict!
Thanks! Normally the proper solution for this would be to disconnect and reconnect the hair, except that it doesn't reconnect accurately after the scale has been applied. Perhaps it would be better to investigate that?
Currently the actual mesh faces only determine the hair orientation and root location, but not the scale of the hair. There probably could be an option added to also take into account the face size, but for now this is not supported.
However there is a trick to get the result you want. So just like you had thought first disconnect the hair, scale the object down and then apply the scale. Now before reconnecting the hair go into particle mode and activate the hair point editing mode. Select all hair keys and scale the hair down the exact same amount you scaled the object (it's also best to snap the cursor to the object center and use that as the scaling origin). Exit particle mode and now connect the hair back. The result should be pretty identical to the original one, but with the scale applied correctly.
Closing the report.