It doesn't actually "suck" to use multiple maps on fighter. But it is true that it's more efficient to keep the number of texture maps on fighters to the minimum. This is because of a concept called "state changes". When a polygon is rendered, the rendering api has to execute a "state change" every time it encounters a texture map which is not the same used on the last polygon rendered. This induces a performance penalty. Since there's usually a large number of fighters in the game scene, amount of state changes can quickly become high enough to cause stalls.
I see the case a bit different for capital ships. You can get away with less state changes if less texture maps, yes. But it's only marginal since there's never the same amount of capital ships as there's fighters. Again on the other hand, less texture maps means less loading of bitmaps by 3d card. But then again, Fs2 doesn't support texture compression. So it's really not that simple.
I'd say, use minimum amount of maps for fighters, and medium amount for capital ships. Then you can do tiled texturing to save texture memory, and the total amount of texture memory is probably less than if you would squeeze it all into a one big map. Also remember that with capital ships they're quite often partly outside the screen. Texture maps used in areas that are offscreen you don't have to process, when with one single map everything would have to be processed always.