I have viktor as my "sub-main" so I kinda know what I'm talking about XD. TBH it really isn't a bad idea because in a typical build you won't have any cd. This is bad because your abilities have very long cooldowns but high aoe damage values. over 34 games and a 76.5% win percentage I can tell you that I feel a LOT more comfortable with scaling ap and hp runes because it helps him plenty in the late game. But that's not to say that cd won't help him more, as it increases your dps and allows your to use your abilities more in teamfights.
You definatly have a point in the CD runes though, its very considerable on him and I can see it doing more than scaling ap. If it weren't for the fact that I use this rune page on Ahri I would probably run the cd runes. Ya know what, as my final stance on this I think that it would be a better idea to run the cooldown runes on him so he can get his ults and lasers back up. 15% Cd is a lot for a cap of 40%