With the exception of a few abilities, buffs that get applied mid-animation or during 'spell travel' time WILL affect the ability or auto in question.
Fun-fact: This works for damage-over-time abilities and debuffs as well.
**Example: Exhausting a Zed that has ulted and ignited a target will reduce the damage of BOTH abilities in real time, even if he has already applied them and the player is 'waiting' to die. **
The only exception I can think of right now is Nami's Tidecaller Buff - this wont affect current autos in motion, as the buff simply enchants 'the next 3 auto attacks'.