Le Campaignne De Faux Promisses names Shivan ships after Judaeo-Christian things. With a few Muslim ones tossed in for good measure. Such as the SD Torquemada
...and more modern ones such as the SF Jerry Falwell.
All kidding aside, generally bad mythological things are used for the names of Shivan ships and classes. The more exotic sounding the better. Volition steered away in FS2 from using all of the Hindu gods/goddesses and decided to stick to just using the bad apples from various cultures except for Greco/Roman and Egyptian. That's because there were more than a few VBB posts about people equating "Destroy Rama" with "Destroy Christ." (i.e. blantant disregard of a culture)
Some campaigns have used other naming conventions, one that's popular is using the Cthulu mythos for Shivan names.
My first joke does have a slight bit of seriousness in it, obscure mythological things from some of the major religions works well. Such as Sandwich's name for a Shivan ship we both came up with, the Bozrah. Generally, the more obscure and evil the name is the better.