Q1: Ship Graveyards are just a colonizeable planet with above average metal and crystal income, thanks to all the scrap. You cannot capture any of the ships, though some mods have their own ship graveyards that do that.

Q2: Titans come back at the level they were destroyed, a bit like hero units in other RTS games. If your titan is destroyed it will also come back at whatever level it was destroyed at. Capitalships are not unique like titans so they do not have this mechanic, though the Advent's resurrection ability on the Progenitor mothership kind of lets you bring your capitalships back as well.