What you could do, is use the new suffix- naming system.
So make a naming theme that is literally just
001
002
003
...
997
998
999
and then combine that with a suffix name theme that only has a single name
Mule
Then when you build your first freighter it'll be Mule 001. When you make your upgraded freighter, just have it use the same themes. Because the suffix theme only has a single name, it'll get reused but Aurora will not reuse already used names from the "main" theme since there are unused ones left, so then you'll get Mule 075 for example.
I already do that in VB6 as some naming themes have loads of names in them so for example my cargo ships and tugs and tankers often share the same naming theme. With the suffix thing that C# brings us, what I wrote above should be possible.