This is a rather interesting question. I would say that it would probably look better drilled out. This will undoubtedly take some time to do. This reminds me of another post in which someone asked how long it takes for some of us to complete a model. Well, I decided while building the German carrier Graf Zeppelin, that I would drill the port holes out because I didn't like the way it looked painted. I have been drilling these out with a slightly undersized drill bit in a pin vise whenever I feel the urge. I have been working on it for about 2 1/2 years now. Also, I should have did this BEFORE I had assembled the ship to prevent damage to the rest of the kit. It is tedious work. 
If you decide to do this time consuming task, plan ahead,and be sure to use references to be able to get the correct look to the finished project rather than have it just look like holes drilled in plastic.  
