They both have their advantages and disadvantages.
I tend to use the 'self sustained parts' technique where almost every part has it's own separate map and you don't need the rest of the ship or it's textures for that one section. This allows me to kitbash and rip out parts easily and I don't have to make whole new surfaces for the same part each time. Since the parts already have custom fit textures, all I really have to do is apply the map to the surface and keep going. I also don't have blank/unused segments of a texture from the parts I didn't pull.
The downside is that it does give you a lot of textures to keep track of, and when it comes to adding illumination (and other options for other games, like BC) it means you have a lot more surfaces to browse through. It's also arguable that it increases the ship loading times slightly.
The other method of 'combined textures' lets you cram everything into a few maps, making it easier to manage and work with. The downside is, if you want to pull a particular part of a texture off one map and drop onto another, it obviously wouldn't fit perfectly and would probably be distorted/altered. Also, if you change the shape/width of one part of the ship (like the hull or wings), that part of the texture may no longer fit properly.
I use Lightwave and Uview for the bulk of the work and since they don't support mod format, I have to reapply textures whenever I rip parts out for a new ship. Of course, since the ship is most likely going to need textures mapped anyway, it's not that big of a difference. I know in 3ds you can simply rip one part off a ship and drop it onto another and everything is still textured, but I personally tend to modify as much of the ship as possible for originality's sake. Besides the fact that I hate the 3ds interface and it's cluttered double-talk menus.
So it all comes down to how much parts swapping/modification you're going to do. If you're doing a one-off ship like a Galaxy or Neghvar (something that isn't inherently kitbash oriented), then the combined maps are a start. If, however, you're going to be swapping out parts left and right (such as a fleet of TMP style ships), and want to keep things self-sustained (each part being independent from the whole), then you could use the holycrapthatsalotoftexturesandwickedmustbeoncrack method.
Of course this is just my personal preference and from the looks of most others' models, I'm in the minority when it comes to the multi-map option. My suggestion is to simply mess around with both methods and find out which one pisses you off less.