Leave the old mortar bed.
That is how tile was laid years ago, on a thick bed of mortar, like a layer of concrete, to prevent cracking.
Just chip off the old thin set adhesive so the mortar bed is flat, no high spots or bumps.
Your new adhesive will fill in any holes or small dips.
If the mortar bed is really torn up, you can apply floor leveler.
Or a layer of thinset, level that, then screw down 1/4 inch cement board.