The contrast between the greebles and the smooth hull is what makes the ships awesome.
Am I the only one who has an absolute distaste for these ships? I mean seriously, I kinda feel that the clashing style between the top, which is admittingly nice, but it's the belly is that really, really, turns me off, which looks like is an atrocious, overly greebled box.
Lol. Taste is indeed subjective.

I seriously hope you have an in-universe justification as to why some of these look like that, because it's driving me nuts.
I do. It all comes down to the historical background of when those ships were designed / built:
In the 64th century, the KessRith and Ssora alien races defeated the (weakened by a plague) Terrans and reduced them to slaves for ca. 300 years. After the humans rebelled and the KessRith Wars started (in the 67th century, when the campaign in question takes place), shipbuilding techniques and military doctrine had to be pretty much re-invented. The KessRith and Ssora ships and tactics became sources of inspiration for the Terrans, while they struggled to develop strategies and designs of their own.
The
Syracuse class cruiser is reminiscent of KessRith designs, with a heavily armored front and dorsal side, while its bottom bears only conventional armor. You can see a similar design on the
Drashok.
The KessRith are pretty much centauroid, heavily armored, reptiles, reminiscent of a cross between a crocodile and a rhinoceros. They have evolved thicker armor on their back and on their upright torso, to shield them during ceremonial and mating duels. Their combat mentality revolves around the 'get up close and personal and pound the other guy to pieces' fighting style. This mentality is also prominent in the way they design their ships: They shield the front and top with impossibly thick, ablative armor, especially designed to protect them against laser fire and slap the heaviest lasers they can get their hands on on the sides. Then, during combat, they close the distance, protected by their concentrated armor, turn / roll to present their armored topsides, and engage in a point-blank slugfest.
The
Syracuse was built as a KessRith ship, with the difference in the fact that it doesn't bear the characteristic KessRith 'fire armor'; it is instead one of the first ships to bear the Terran 'White': a superdense/reflective material armor, found in every Terran ship since. The
Ultor and
Ravenna are
later designs, more 'Terran' in style, with armor distributed evenly across their smooth hulls.
The U and R have nice lines but look a little bland in comparison.
The Ravenna is pretty hi-poly for its length, actually. The Ultor looks bland because it is: it WILL be rebuilt, but maintaining the 'smooth hull' style.