Depends on the air flow design of the case, if they were an addition to a normal case then, it was cuz some engineer decided they should be there for that cases airflow. Personally I don't think alot of computer case designers ever went to mechanical and thermodynamic engineering classes but I may be wrong. 🙂 The best way I choose to look at it, is are they trapping heat from a heat source? Do they channel air to an exhaust port?
Are they preventing heat from a known heat source from reaching a temp critical area. But honestly most cases with and exhaust fan and a inflow case fan handle most heat situations just fine. Only exception to that rule is the new 1GHZ Athlons, they run between around 50watts. Think about a 50 watt bulb in a box. Its gonna get hot! So heat management is gonna become critical the faster/hotter the new processors get. A top exhaust becomes a REAL good idea, since heat rises we shouldn't try to make it go down to get out. That fights nature. In that fight nature wins. Well I been rambling.
My ideal design for a case would be two fans blowin in from the bottom, a front top exhaust port to isolate the drives heat from the processors heat. And a rear very top mounted exhaust fan to draw the main heat sources heat away and create an air flow.
DOH I feel like a moron, I thought you was talking about shrouds that cover the card area. Yeah definately keep your backpanel slot covers on. You want your air to vent top not bottom.