On (1) I want to do a drydock mechanic with a bit of a tech tree that acts like Space Station Commander (which is completely concerned with repairing and servicing ships). I don't have a good design for this part of the game yet. For now pop into Debug and push the hull to full (there's a button)
For (2) I designed this to be a low-aggression game so you outrun the Pirate or retreat to a zone around stations to scare them off.
Unrelated, since you're checking the game out I just want to flag I'm going to drop Tier 6 entirely, since the Galaxy harvesting tier is the same mechanic.