I really like the idea of random events happening in hyperspace, and some of these suggestions are great. A few more/slightly different ideas:
- Quantum Field Transmogrification: After passing through a hyperspace quark storm, all of one resource is converted to another resource
- Timeline Collision: Your hyperspace lane intersected with one from an alternate timeline! A duplicate of one of your crew members is now on board (with a goatee, of course!)
- Gravity Well: A miscalculation has brought you too close to a gravity well, forcing you to drop out of hyperspace. You now must deal with the nebula, star, planet, black hole, space-pirate-trap, etc. before you can continue on.
- Hyperdrive Malfunction: The catalyzer on your hyperdrive's compression coil exploded! Until you can buy a new one, or have an engineer fix it, your speed is dramatically reduced.
You might check out the Firefly boardgame for some ideas. They have two decks of event cards for when you travel through space: