For wrecked ships you’ll only want to swap if it’s a significant upgrade. For mine, my starter ship had 15 cargo slots and was worth 330K, which is like 250K in trade value. The wreck I swapped to had 23 cargo slots, and 8 tech slots, and a value of 2.8 million units (once fully repaired). That was a big enough upgrade to tempt me…but I am still paying to repair the last few cargo and tech slots that were red to start with.
It costs units (money) to repair those, and the cost rises with each slot repaired. I went broke just getting my wrecked ship up to 17 cargo slots, two more than my starter. Since then I’ve spent multiple “runs” doing mostly mining/salvaging for cash and used the income to repair more of my ship. I’ll have probably spent close to the 2 million units it’s worth in trade by the time I’m done, but it’s been worth it for the improvements.
As for the ships systems, they are usually pretty low cost (in materials) to repair. You can deconstruct anything you’ve added to your starter ship and get back half the materials, then rebuild it in the new ship (assuming you have slots available).
My first space station had no pirates or aggressive ships around it at all, so I think it’s just luck of the draw.