I currently have a GTX 980 that's 7 years old for reference, and when it's splitting the source video into frames, it seems to squeak for each frame. Is this normal for the program to do or should I refrain from using the program due to this? Also if it's not due to the graphics card, then what?

It is called coil whine. Really common on GPUs, can even happen to SSDs or other electronics. Of course you gonna hear more whine on load; that is, each frame.