If your ship gets destroyed you will get a replacement with the credit cost taken from your account (or the faction treasury if you don't have enough), you will lose anything fitted on the ship and its hold contents will be scattered as adrift or potentially destroyed. You will also lose any ships that were docked in bays and will receive a soul currency deduction - which could put you into a negative balance.
There is also a chance some crew may die and some of your factors will change.