Hi nbucska
I disagree with your No,
That would be true if the computer program you mentioned used no processor time, no RAM and or virtual memory, no video display etc.
Depending on the priority of the interrupt depends on when they get serviced. What if you program is using a higher priority device?. It is for example possible to have a rogue peripheral which continually interupts and hangs up the PC. I suspect it would be the same with a program using a device. So I still say a program used to measure the performance of a PC will affect the results. However this may be factored into the results.