Yeah, i never understand why riot removes scaling like this on abilities which normally don't get used.
No one cares that Jayce has 25% AP scaling on his hammer W. Does it need to exist? No. Does it need to be removed? No.
If there was a variant of the play style which slightly utilized the scaling. What value does removing it give to AD jayce in order to nerf AP jayce?
Now obviously this is an extreme example, but unless they design the skill in a way which offers the same damage potential as the "primary" build, then it will never be a problem, and simply exist to offer variety in the game when it gets dull. The reason i say this is because AP Yi existed, but it was only because the Q reset on kills. They could've nerfed the ratio or removed the refresh, instead they outright removed the AP scaling.