Optional Rule for 'Small Hex' Games: Any time two NPC vessels enter the same hex roll d100 for each ship. If both rolls come up the same number, the ships make contact and both take the number rolled in hull points of damage.
Fleet Captain does not come with a set scale for either time or distance. Individual GMs, scenario designers and player-empowering anarchist collectives can work such things out for themselves. Or simply do what the designer does and remember the MST3K Mantra: Repeat to yourself it's just a show, I should really just relax.
But there are times when the size of one of those hexes of empty space really matters. One is when you want to know if ships can accidentally bump into each other or not, hence the optional rule above. Another is when you want to put a planet on the map.
If we're fighting a last ditch effort to defend Earth from the forces of Omicron Persei 8 it's important to figure out at some point whether or not Earth fits on the map. Perhaps you print out a custom counter that's exactly one hex wide. "This counter blocks line of site and anyone entering this hex must make an Avoid Hazard maneuver or crash into a randomly determined city in New Jersey." Or maybe you cut an old globe in half and slap that puppy down on the map. You'll need different rules for that to cover the partial hexes peaking out beneath the hemisphere. Another possibility is that the battle is taking place so close to Earth that any vessel exiting the right side of the board at more than Drift speed crashes into the planet.
Or perhaps these hexes are friggin' huge and the Earth is just another dot in hex 1213. If I recall correctly,
Anyway, my point is that "Oops! I got my destroyer in your frigate!" is funny. But it shouldn't happen too often. Space, after all, is really, really big. Besides, if you want vessels crashing into stuff, that's what Improbably Dense Asteroid Fields are for.