That is a typical Sci-Fi thing. Come on, realistic space combat has only been featured in books thus far since it would be boring. No sounds, vast distances, incredibly high speeds and I don't want to start talking about the physical properties of lasers and stuff.
Bottom line, this is typical of design. When creating something visual, you aim for the following: It has to look good, sound good, needs a recognizable shape and appeal to our intuitive understanding of things. It usually does not make sense, especially for something technical.
Although I do agree on the Vorlon "Windows". My guess is that it is probably related to the changes on the Vorlon's nature, in the pilot ambassador Kosh has a hand! Back in the day, they were probably just another alien race.
Regarding our approach to such problems... Zathras fixes. Poor Zathras always fixes.
In that case, a removal of the hangar is probably most appropriate (potentially replacing it with a dock point).