Thanks for your replies!
You could try the 'xev' program (in the x11-utils package, well in debian at least).
Run it from a terminal and watch the output when pressing the mouse-wheel. You should see ButtonPress events for the mouse-wheel.
This will tell you whether the problem is in the X server (or Xlib), or the problem is client-side (SDL or ioquake3 code).
In xev I can see the scroll events while moving the mouse. If I couldn't, I should experience the problem in other applications (such as Chrome) too, but I don't. So that would mean it's in SDL/ioq3 right?
I learned to use the buttons at the side of my mouse to change next/prev. weapon, and created some binds for specific weapons.
Hmm if those buttons work but scrolling doesn't, isn't there some way to map/bind the scrollwheel to these buttons on system level? Or generate another event (like a key press). With an external application which, like xev, does notice the scrolling events, wouldn't this be possible?