You can get cosmetic shards for skins you already have as well.
They do intend to do something for players with all champs to make the champ shards/essence not useless eventually, but no word on what exactly. For awhile it was going to be involved in unlocking mastery levels 6/7, but I'm pretty sure they scrapped that idea (as people wanted something more mastery related rather than luck related to unlock those).
One minor perk in the meanwhile is you can save up 3 to reroll into a new champ when one comes out, although that's probably moot since those with all champs probably have tons of IP anyway.
Skin shards for skins you already have are sortof useful as you probably won't feel guilty about disenchanting/rerolling them, which I know for me personally is an issue. I have 3 skin shards I probably won't ever actually use, but I don't want to disenchant in case I ever come around and start playing the champ, and I don't want to reroll both for that reason and because I'm worried I'd get an even less desirable skin.
(If you're an intense collector who had all the purchasable skins, rerolling 3 skin shards is assured to give hextech annie, so at least theres something there for those people, although I suspect they're a minority.)
I figure they have it balanced around the existing uniform probabilities, so rejigging it so you can't get loot you don't want/need due to already having it might throw off their balance intentions.
