The shatter spell says that it does one of three things: It either "creates a loud, ringing noise that breaks brittle, non-magical objects; sunders a single solid, non-magical object; or damages a crystalline creature" (emphases mine).
The effect created by a wall of bones spell is magical because the effect's on a time duration: the magic ends when the spell's duration expires and, for example, even if the timer is still going a successful dispel magic spell will dispel a wall of bones effect prematurely, and the effect winks out in an area of antimagic. Hence a wall of bones effect isn't a valid target for any function of the shatter spell (especially not the last).
The wall of stone spell, on the other hand, has an instantaneous duration: after the spell's resolved, the magic ends, but the spell's effect remain. And what remains is a totally normal nonmagical wall—a dispel magic spell can't dispel it, and it's unaffected by areas of antimagic.
Also, to be clear, the shatter spell typically can't affect a stone wall: a wall is usually neither a group of brittle objects nor a lone object. However, a GM may allow a shatter spell to target a wall section.