The archive.org project is just titled "SimCity NES Prototype Archive" and the archive itself makes no reference to "open source project" so I assume it's just another misguided journalistic edit as well.

The archive does include a directory with disassembled ASM of the original NES ROM (with some added comments) but disassembly falls into a different legal realm than GPL/actual source code/open source remakes. Between that and The Internet Archive being excepted from DCMA, being excepted from copyright protection removal law, and having a long legal history of preserving copyrighted works I'd wager there is nothing to be worried about for that archive.

Also cool work on the original port and particularly Micropolis. I remember having a lot of fun with the code when it first released.