I like to think of them as bureaucratic failures. The UEE ordered the design of the destroyer but before production, they had to cut back their funding per ship. So they scrapped the original design and came up with something that fit the original production line and met the UEE's new specs. Unfortunately the dorsal section of the ship that mirrored the ventral had to be scrapped, leaving a relatively underarmored and undefended belly with thinner armor.
Helps me sleep at night. =P