We perceive visual stimuli as distinct events (up to a certain frequency), but when hearing, a 40 Hz sound isn't perceived as 40 individual sounds per second.

Perhaps because it isn't? Waves are not discrete structures. 40Hz means you have 40 wave cycles per second, not 40 discrete sounds.

That's kinda what I'm getting at. My understanding is that brain waves are more akin to a CPU clock, with various processes being synchronized, than to a sound wave. If that's the case, then you wouldn't have any reason to expect sound to make a difference in your brain's clock rate, but you could reasonably expect light pulses to.