See above: I hope the situation is more clear now.
So I tend to close this bug as wontfix, and just mention in the documentation (NEWS at least) that people who remap header-line or mode-line need now to remap the new -active and -inactive faces.
Ok, I get what you're saying here, but I don't know that I agree with this:
"...people somehow expect that remapping the header-line face will affect header-line-active and header-line-inactive." I'm not sure why it wouldn't be expected.It shouldn't be expected for basic faces.
Or we could do what the mode-line case did originally: leave the active face to be header-line and define header-line-inactive without inheritance. This will at least let existing remapping of header-line work as it did before.
For the same reasons, I would prefer to go back on the mode-line-active change, but I'm not sure this is practical at this point.
This would mean that the base faces, header-line and mode-line would be eliminated.
No need to go that far. These faces are still useful, because they allow to define the inheriting faces more compactly, and allow to change the definitions easier. Inheritance still works on the defface level, even for basic faces.