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Will items / cargo be in visable storehouse or will they be invisable "imaginary inventory" esque?
Visable cargo will be in stores so you can see before you buy, and their inventory will be visable from the storefront, basically, but for just storing stuff, then seeing it in a storehouse? No.
Actually physically loading cargo into big ships? -
We don't want a click button, get inventory. We want it to take time. But we don't know how that's gonna work yet, but the big picture is it will be automatically done by machinery - note on this, they also said that specialized ships (such as the argo) can offload cargo, if some players want to be a dock work
Scavaging - getting parts from ships (engines, gravgens, etc) and Scrapping - destroying ships for metal. Can also pull guns off broken off wings, if the guns not too damaged, as example. Different parts of ships will have different profits, which means if you need to get in and out it'll be beneficial to know what's more cost efficient
Hazards when Mining and Cargo running, besides pirates?
meteoroid showers, debris fields, micro black holes, all this can provide information, that can be sold. Leading to more work for other players / more interaction. Also your ship will degrade over time. So maintain your ships.
How will destructible props be repaired over time? I.E. Olisar's window gets shot out, how does that 'reset'? -
Important items will stick around and be persistant i.e. ships on a planet if you leave. Some stations won't be destuctible to prevent griefing. Missions are generated for A.I. and players when something gets destroyed to repair it. Otherwise, A.I. will repair damage such as windows getting shot out, or cleaning up trash
More loading / unloading cargo questions .
there will be physical, as well as automatic loading / unloading of cargo. There will be in-gameplay reasons to unload cargo by hand, but it will be small hauling jobs, they used smuggling a lot as an example, getting out of your ship and smuggling small items adds a new stealth feeling...., but as far as like Hull hauling, all major ports will have automatic unloaders.
Will we be able to move between professions fluidly, or will there be like a rep system?
No gatekeeping, you'll be able to switch fluidly, no RPG rules... No levels, but there will be reputation, so for example, no one will give you expensive shit to haul, until you haul enough stuff to prove your worth
Ship based mining in 3.0?
Yes. Fundamental mining in 3.0, including the prospector
Do you need rep to do a job, or just the right ship?
the more expensive / lucrative jobs require rep... But otherwise you just need the right ship
Will there be an autopilot that allows me to get up and move around?
Yes... you'll need to for maintanence on long trips