PCI (and PCI-Express) were designed to fit into cases that also contained ISA cards, but still use the same brackets. This lead to them being create with the opposite handedness.
I.e. the answer is historical reasons.
It is my understanding that usually it’s because the CPU is above the slots, so they are trying to keep the heat-producing components as separated as possible.
I think a very key point has been missed by the OP.
GPU fans typically pull air INTO the GPU, not blow it away! The fans are designed to be pulling the coldest air INTO the GPU to actively cool it. The coldest air is at the bottom of your case. See image:
GPU fan orientation
So the air IS going in the direction you’re describing, its routing the air up AFTER it has hit the GPU, which is when the air gets warmed. So even though it may look to you like the fans are blowing “down” they are not. They are sucking in the cold air from the bottom of your case and releasing air at their sides, which then floats or is blown by your other case fans, out the top/sides of the case.
To add what everyone else is saying — hot air rises; you want the coldest air in the case flowing into your video card. And that air is the air at the bottom of the case, away from the CPU. This is why the fan faces downward. HTH!
- you can buy inverted cases that flip the cards.
- It is true that the coolest air comes into the bottom of the case, and a downward-facing fan could take advantage of that air, however i’m not sure this is a REASON for this design so much as a circumstantial benefit.
- Having GPU below CPU keeps the GPU from getting more heat from the CPU, inverted boards/cases (mentioned above) are dumb unless you’re more concerned about CPU temps than GPU temps, which you shouldn’t be.
- The alignment of the bays in the CPU is such that the space granted for a slot lies beneath it on the rear panel, so it is necessary to put the components (including the cooling fan) beneath, simply because of the historical design of PCI/VGA slots. Why THEY had THEIR components (transistors, etc.) facing downard is a mystery, as this design does trap warm air generated by the components, however heat was a non-issue with most early computers using these slots. Enthusiasts didn’t come along until well after the slot design had been established.
So if you REEEEALLY want your fans facing up, buy an inverted case with board on the left…but this will put your GPU above your CPU with any normal mobo layout so air management is important to ensure your GPU fans get cool air.