Copywrite gives the holders the ability to begin legal action against anyone they feel violates it. It is up to the holder to decide how to enforce it. It looks like Konami have made it clear that they will not challenge Shadow Moses, and will even endorse it, therefore all is well.
Don’t let this put you off developing your own IP. If you’re that concerned, you can take a zero-tolerance policy and have a blanket ban on remakes, fan-made spin-offs and the like. As long as you can prove you have not authorised others to use your copywrited material, the law will be on your side. If you can prove that the unauthorised usage has resulted in financial loss, you can sue for damages.