Reputation will be kept. Only physical in game purchases, looted items and aUEC will be wiped.
Agree on the ships. I have just ccd my Cutlass for the Prospector.
I have the MSR for multi crew and transport - I felt the Cutlass was a ship to buy in game if needed but the Prospector opens up Mining sooner given its cost in game (hope that makes sense?)
I think the Hurricane, Mole and some sort of bulk transport like the C2/M2 mighr be usefull to aime for in game. I would say Hurricane is the No 1.