So you can use autopilot OR you can use manual control in any system and at any time (unless your navcom is broken). But autopilot just takes you where you tell it to go - it's a dumb autopilot. It won't automatically navigate around asteroid belts or dangerous nebulae, for example. Regardless of which you use, you'll ALWAYS be wanting to check your emissions, go dark when you suspect pirates are nearby and stick to benign nebulae for extra cover. Your choice in navigation method doesn't really impact upon the likelihood of them finding you too much. It's more about which systems you choose to have on / making noise and where you choose to go. The key really is to only use thrusters at moments when you're SURE there are no pirates around or you're in a nebula. OR when you're in a pirate's baffles - they can't see behind them, but neither can you.
Map data for sale isn't really a feature we've discussed. I can see the value in it, but I think the stand-in for that will be that you can sell data gleaned from scanning planets for bonus money (using science probes). That'll be the most likely reward for exploration. We want to reward players for exploring, but it isn't an exploration game per se. Key things you'll find when exploring different systems are: a) more trading outposts with more contracts for you to unlock, b) more planets and moons to scan for bonus coin, c) cargo pods adrift in space (more common the further away from civilisation you go), d) derelict ships to search and scavenge from and e) communications beacons (but I'll refrain from explaining those in detail here, lest I spoil the fun of discovering them.