In general, a ship will only have one type of FTL drive installed due to both size and cost restrictions. However, a Heavy Cruiser or larger (I'll probably have to get around to size classes now, but in general fighter <<<shuttle <<frigate <light cruiser <destroyer <heavy cruiser <battleship <dreadnought <juggernaut) would have sufficient space to mount two FTL drives, at the expense of whatever would normally occupy that space (usually the hangar). Subspace drives can be built small enough to fit on a fighter, but their cost and size scales quickly with the size of the ship. It's actually not possible to add a secondary drive to a Juggernaut if the primary is subspace.
As far as cost goes, Warp drives are the cheapest by far, so most twin-drive ships (which are still ridiculously expensive, but they exist) are Warp/something else. Subspace drives are in-between, although their cost increases for larger ships. Hyperspace drives are expensive and take up a the most space, but they don't scale much with ship size and so are suited for larger ships. Hyperspace drives are actually not used much, because their performance is so similar to warp drives. The main advantages that hyperspace drives have (besides actually becoming cost-effective for Battleship-class and up) are the ability to avoid collision with Realspace objects and the ability to actually hide in hyperspace without moving. It's actually possible to hide an entire Star Base in hyperspace, keeping it supplied with hyperspace-capable ships.
Now that I think of it, I'll be adding this to the FTL file under the heading "Which FTL is right for you?"
P.S. If you're wondering how those pirate fighters showed up in the story, they don't have FTL drives at all. The pirates took advantage of the warp bubble generated by their LC.
tl;dr: One drive per ship, the file will be updated soon to list details and exceptions.
