They can be and should be both. The air flow design is for the entire machine and heat flow from CPU and GPU are often moved by heatpipes.
If you feel the fan is slower than new, why not get it replaced?
I have an MSI 62GL 6QF laptop. The fan on the left(while facing the monitor screen) needs to be replaced. Can anyone tell me if it is the GPU or CPU fan? I know very little about computers. The fan is running very slow.