As far as changing other things in the shiplist goes, you can mess things up if you aren't carefull.
You can change stuff like "War_Destroyer" to some other already used class. Like "Frigate", for example. It will change the way the script sees the ship, but won't stop it from using it. If, using the above example, the script is looking for a frigate to match up against you as an AI opponent and you've changed the "War_Destroyer" to a "Frigate", it might see it as a perfectly acceptable opponent (There's are other considerations, but let's not complicate it beyond your actual question.).
To the best of my knowledge you have to use one of the classes that's already in the game. The choices of classes is hard coded, as far as I know.
Changing it to "Special" will make the script overlook it, unless it's specifically scripted in. Example: If the F-DW is specifically written into the script, then it will still use it, regardless if you've changed it's class.
I believe that the class also comes into consideration for the shipyard builds in campaigns.
I think that this is the "library entries" that you were asking about. They're in the "help.gf" file. They aren't hard coded and you can edit them freely. Here's the stock OrionOrion text and an edited one where I've changed them to Tholians in game.
MataAssets\Clientsettings\Help.gf
Stock:
[Race/Orion Cartel]
UpdateData = 8
Text = "This Group claims to be the original Orion pirate cartel. This may actually hold some merit since there are many ex-naval officers serving on board Orion pirate ships. The Orion government denies any connection to this cartel, claiming that the "Orions" are just a collection of thugs and space pirates. This does not ring entirely true to some, as investigators that have found evidence of Orion properties being left alone while "enemies of the state" seem to have cargo raided on a regular basis. This cartel is very powerful and is in direct competition with the majority of the other organizations. The Orions are elitist and sometimes find it hard to recruit some races they find to be beneath them. The Orion ships have photons and phasers as their main weapons, but also employ disruptors, missiles, plasma, and cloaking devices."
Custom:
[Race/Tholian Holdfast]
UpdateData = 8
Text = "The Tholians are not native to our galaxy, but migrated here from another. They are the survivors of a race that once dominated their native galaxy, the exact location of which is unknown. The Seltorians, who held the title of "most trusted subject race", revolted and overthrew the Tholians. They fled their home galaxy, rather than face the wrath of the beings that they had ruled over so harshly, by constructing a Dyson sphere that encompassed their entire homeworld and moved it with them to our galaxy. The Tholians occupy a sector of space claimed by the Klingon Empire that has borders with the Federation, the Romulan Empire, and the Klingon Empire. They are under constant harrasment from the Klingons who, even though they have the military might to easily sweep the Tholians from their space, haven't been able to spare the resources to do so. The Federation has also let it be known that they would not tolerate such military activity on their borders, compounding the Klingon's difficulties"
I hope this helps you.