FWIW, I think that the fan in my Cube at least accomplishes something.
I have two Cubes, and I've upgraded both with GEForce 2MX cards, although the desktop version in both cases and not the Cube specific version. As most Cube tinkerers probably know, the faceplates on these cards are interchangeable with the stock Rage 128, although the desktop version of the card has a comparatively small heatsink compared to the Cube version. The desktop cards have a reputation for running very hot in the Cube. I found this out the hard way, as I made the mistake of disassembling one of mine immediately after powering it off once, and the heatsink was hot enough to raise a blister on my finger.
In any case, as I mentioned, on one of my Cubes I have an MDD case door fan connected to J2 and dangling in the space between the logic board and the back of the video card. This really isn't where the airflow should be to cool the video card, but I figured it wouldn't hurt anything.
After using the one with this extra fan for a little while last night(both my Cubes have base fans tapped into the molex connector on the optical drive), I found the video card at least a little bit cooler than on the one without the fan. It's not much of a difference, but at least I feel like this fan is accomplishing something.