In order to actually make a copyright claim on a reproduction PCB, you have to argue that the PCB reproduces a copyrighted work, such as the contents of a Mask ROM. However, if you can avoid needing to reproduce those ROMs, then you're free and clear of copyright issues. For example, you could just provide a ROM chip socket matching the original board, or ship a flash chip with a workalike ROM (if that is an option by the time SCOTUS decides Oracle v. Google).
The only avenues left would be trademark or trade secret protection. Apple loves sticking their logo all over replacement iPhone parts, and for whatever reason Chinese clone part manufacturers continue doing so. The Shenzhen markets like that, even though foreign part importers beg them to stop doing that. Presumably, however, anyone cloning an SE/30 board in the US would know to not stick Apple logos on the thing. Trade secret protection claims would also be rather spurious as the machine in question is very public, you didn't sign an agreement to keep the machine's design confidential, and reverse engineering is legally protected within the guidelines I stated above.
I'm wondering, if this replacement board doesn't have them, how was that done?
Like this: http://pc-restorer.com/wp-content/uploads/2014/02/SE30-bad-c...