Why did Mordekaiser's enemies hide his remains in the blessed Isles instead of destroying them? Did he put some necromantic spells on his remains? There are other questions about him interacting with the other shadow isles's champions . I put one thread here,if you have more information .that would be welcomed.
Edit: my bad, it's bothering instead of bodering!
You could grind it to dust, the liches would still find every speck of dust.
Hell, I doubt Morde could ever truly be stopped. Maybe throwing his bones into the void may give valoran a few hundred years without fear of the Immortal revenant.
I'll try to answer both.
We don't know bits about the spell that bound Mordekaiser to the undeath, what we know is that he is more powerful than what even the spell was intended for and that he is the only of the spectres able to rise other spectres. His remains (the skull to be precise) might have been too risky to destroy or even impossible to by any known means so the only chance was to scatter and hide them hoping that he would never return. Plus we know that denying his resurrection doesn't really kill him as he would just need the full skeleton again.
He has control over the will of the victims of his curse and over the Black Mist but this does not have influence on the other champions of the SI as they are driven by personal matters: "He looks down upon these newly formed undying spirits as a lesser breed, for he chose his path freely, while these others are merely lost souls. Nevertheless, he sees their use; they will be his foot-soldiers in the conflicts to come" The quotes of the Altars are just outdated but you can still consider them valid. Hecarim is following the will of the Isles which is bound to the will of the Mist and probably the Mist doesn't like to be toyed with by Morde (not that it can do anything about it "evil metal laugh"). About the "are you also a prisoner" quote it might be the Altar trying to taunt Mordekaiser not knowing that he chose undeath himself.
Perhaps they didn't know how to properly destroy them? Beyond the magic, do you know how to properly destroy an iron helmet? The atoms still exist if you smash the helmet or melt it down.
There was probably some reason as to why, for instance perhaps the bones were enchanted in such a way that only destroying one of the bones wasn't enough, and they needed to destroy the skeleton, which the Liches claimed before anyone else could. Alternatively maybe they tried and the skull just couldn't be broken by any of the magic they had at their disposal, so they locked it away until they could find the means to be truly rid of it.
Well the identity of the thief is overall unknown,so it is possible that the thief had his/her own plans with it.
Alternatively the skull might have been protected by some spell that prevents its destruction(or could cause severe problems if it got destroyed)
