The trick I've seen with any reference to FTL travel is that unless the ships are actually measuring distance in light years per jump (Ala Battletech), the jump nodes are placed such as to make an interesting plot, or even picked at random.
A good example is the game Fading Suns, which uses a very similar style of space map as FreeSpace 2... In essence, the distances mean nothing, and the planets are linked by set jumps.
This frees up the author from having to be 100% accurate with true distances and space limitations on a map, although it also inadvertantly makes it nigh-on impossible to crete a "true" map.
Also, using hyperspace gates or the like introduces the theory of "lost" planets, and it is a heavily used plot device whenever planets are such linked.