Didn't we all think that, when we first saw the original series?
There are really not that much locations on the Enterprise
(e.g. neck dorsal) where the angle of the Jefferies Tube seems to be a structural necessity.
Come to think of it, the scene in "The Ultimate Computer" could be a hint for a Jefferies Tube leading up to the nacelles. The basic question remains, of course, why you should have certain control components on one side of the ship exclusively.