Yes, Tim has said that it doesn't have any apperature (I have the quote, just awaiting permission to publish it). Adding a additional opening would require the addition of an airlock, armor and a lot of space consuming equipment. Also doors will always be weaker than fixed armor, and hence a potential weak point. I suppose if the fighter jammed up the recovery bay that it wouldn't be too hard for them to go in the launch bay.
Those openings are actually quite large (have to look in more detail to get a number) and should leave plenty of room for a mammed fighter to make its way through. I would also assume that there are aides in the bay to grab, slow and dock the fighters (sim. to the cables used in modern aircraft carriers) so that they can come in without having to slow too much.
As to why the maintenance shop is extruded as it is, you'd have to ask Tim
