Good questions, and they're tricky ones to answer, but I'll have a go.
We've designed the star systems so that it should take you about 4-5 minutes to get from one side to the other, and you can jump in between each system, but have to be a) in the closest quadrant of the system you're in to the one you're jumping to and b) not near any sources of gravitational disturbance, so a fair distance away from planets, moons or the star which is in the middle of each system.
Although we realise that nebulae should in theory be jaw-droppingly huge and not occur within solar systems, for gameplay reasons we've added both them and asteroid belts to work as (as you say) 'clouds'. Every solar system will have at least some stellar objects in them, and some of the harder ones to traverse will be so filled with nebulae and asteroid belts that you'll be hard-pressed finding some normal space to navigate in.
Typically, you won't find that you've got an incoming missile, so decide to make for the nearest asteroid belt (although that is a viable strategy). Typically, you'll be navigating through a nebula or asteroid belt so as to avoid that incoming missile in the first place. But having one within 2 minutes time of your current location at any given moment is a fair assessment.
I hope that's answered your questions, but feel free to hit us up with more!