To say that late game Q damage is changed by 30 is a HUGE misconception.
Let's say that a late-game Fizz has about 600 AP(no lich bane built to have less things to add in), and about 100 AD. A max rank Q with the .5 scaling would be 300 more damage, plus the base damage and on-hit effects applied like normal on Q, which would total (70+300+100) Magic Damage, which would be 470 damage.
Let's change that to .3 AP scaling. Now with the Late-game Q, the AP scaling is 180, and the total damage is (70+180+100) Magic Damage, which would be 350 damage.
470-350=120 damage change on his Q, which is a much larger number than 30.
If the Ult Debuff were to be applied with .5 AP Q, a Q on a marked target would receive (70+300+100) Magic damage, increased by 20%, which would be 94 extra damage, so the total damage of a Q to a marked target without applying magic resist would be 544 Total damage, which seems reasonable for an assassin in the late-game.
Let's bump down the Q AP scaling to .3. A marked target Q would take (70+180+100) Magic damage, the 20% damage would be 70, so the total damage on a marked target would be 430 magic damage in total, which is more than 100 damage less than the .5 AP scaling of a marked target, and still does not even do as much damage as a Q to an unmarked target with .5 AP scaling, and I would hesitate to call an assassin come late-game.
So yes, .3 and .5 as a matter of fact, do make a difference.