I lived with that for 10 years with my YJ and it never bothered me. I loved everything about that Jeep.The holes were cool...it's all about visibility.
Having said that, I hate half doors. They suck eggs. Having to unzip the window to grab a bag at the drive-thru window? No thanks. No where to rest your arm while driving? No thanks. As far as I'm concerned, either run with the doors on, or take the doors off. I've never understood the appeal of half doors and the one I drove pi$$ed me off after living with it for a day.