To be honest, a large number of the names are just collected syllables. I'll find a few single-syllable word pieces and stick them together, which is ironically the same way that a lot of the ships are being created now. Here, let's try an exercise, and see what weird and futuristic ship names we can come up with.
First, we have to consider if we're making this thing brutal or sleek. Neutral is another world altogether, because you have to find a balance between the two. Let's assume we're going with brutal, like the name for a heavy cruiser on the NDC side, perhaps.
In the "harsh" or "brutal" phonetic category, we have a lot of plosives (yes that's a real word). Plosives are phonetic pieces that do exactly as their name suggests: they "explode" from the mouth. These include:
Ka
Keh
Kee
Kai
Ko
Cha
Chai
Ta
Tae
Tai
...etc.
There are always a few neutral-sounding phonetics that are useful for rounding out the sound of a name and making it sound more natural. These softer phonetics are good for finishing off the name, or adding a syllabic break in the middle of the title. Many of these use vowels as their primary focus, as well as consonants that have an easy, flowing sound.
Ora
Aree
Ior
Io
Aro
Era
Eara
...etc.
By combining the plosives with these softer sounds, we can make some neutral-sounding names like Kaiora (KAI-oh-ra), or maybe Taelika (Tai-LEE-kah).
But we're here to make rough-sounding names, so let's add some more plosives and chop in a few more syllables to make the transition between phonetics quick and somewhat grating.
Tessecharach (TESS-ah-kar-ack)
Chaitemtua (KAI-tem-too-ah)
Kaennack (KAY-nak)
These are, of course, just nonsense words, but they demonstrate how simply combining almost completely random syllables can produce fantasy names with relative ease. Almost every word in the english language can be easily broken down into its constituent phonetics and analyzed to create new sounds and names. In the word "Kodiak", you can see how the leading "K" provides an introductory plosive, quickly giving the word a harsh attack. "Odi" functions as one of those smoothing phonetics, but remains somewhat to-the-point and keeps the word aggressive. Finally, the word finishes on another plosive, "Ak". The word Kodiak is very easy to interpret as a sign of at least moderate guardedness and aggression, even if you've never heard of the animal that has the name. Characters given the name of Kodiak are usually portrayed as brave, less-than-talkative hard-edged warriors with a slight vein of vengeance in many cases. It's a quick, harsh name that implies power and strength.
Conversely, I'm sure that you've all heard the mumbo-jumbo about the word combination "Cellar Door"; supposedly the most beautiful combination of two words in the english language. The reasoning behind this is simple phonetic analysis, which reveals that the word has almost no harsh plosives. The closest it comes to such is the beginning of the "D" sound in the second word, but this is offset by the way that it can be segued into from the previous phonetic, "ar". "Sell-ar-dor" is very easy to pronounce, and easy on the ear hearing it.
The human ear listens for three things in the tone of pronounced language: Hard sounds, soft sounds, and neutral sounds. Hard sounds suggest violence and threat. Soft sounds suggest compassion and tenderness. Neutral sounds suggest comfortable conservatism; a lack of change as could be influenced by either soft or hard sounds.
Ships such as the Chrenari or the Gammadon are combinations of neutral and hard phonetics, giving them a slight edge that says "this thing is generally an icon of comfortable neutrality, but has a hidden hard side that should not be trifled with." Basically, you can engineer a name to give your audience whatever kind of presuppositions that you so choose. Give a hard name to a defenseless freighter, and people will simply assume the crew must all be roughnecks. Give a soft name to a military ship, and people will likely assume it is diplomatic in nature.
True, there are several names from older languages that follow a directly contrary system, such as "Ares" or "Zeus" which are both composed of soft phonetics, but it is an understanding of their mythology that infuses a sense of power into the word in such a case, not the core pronunciation.
There's a lot more in terms of phonetic engineering, such as why "Slartibartfast" sounds like a dirty word, but that's too much to go into detail on.
Addendum: Of course, some of the ship names are just based on what I want their function to be, using quick-and-dirty pulls from the dictionary. The Scimitar is named as such because of its asymmetrical design, and its ability to cut a swatch of destruction through an enemy fighter brigade.