Unfortunately, I am not too sure if your case will be compatible with a 140MM fan. I've owned a Rosewill Blackbone in the future (brother has it now) and it only has a mount for a 120MM fan.
From my personal experience, covering the holes in the side won't provide better airflow, but will make your internal ambient temperatures a little bit hotter
I would just leave it as is! (Though, you might want to cover it up with a bit of mesh..I remember this was my primary intake of dust when I used the Blackbone