Mostly because older games ran at a much lower resolution. I'd suggest just doing everything at 1x pixel size and then scaling up to 2x after the art is done, or scale up in C2.
Another thing to keep in mind that a lot of indie devs seem to overlook is making sure the game itself runs in a lower native resolution, otherwise you'll end up wasting CPU/GPU resources to render low res art. In C2 you can turn off HQ scaling as well, which will give you a more accurate low resolution appearance and better performance.