Pretty sure that it's intentional. You own that freighter, after all; you're given pretty free rein as far as how much modification you want to do.
Of course, you could strip it to the bare deckplates and then buy a new one after the next pirate rescue mission. Would hardly be sporting. ;-)
Very true. These things in hull, I deconstructed, came with it. Only thing I added was 3 stations, and 5 away team rooms, and a vendor. And with 1.63, a large refiner. These boxes and loot crates were always there. I got antimatter, with ea decon.
If they reappear, ea scum save, or ea star system jump, this is free travel. Only need to encase the antimatter from one, mine had 2 v1 cylinders and 1 loot crate. Thats 3 antimatter, a pop.
Not very sporting. But fuel efficient.