I have the same problems, hard coding the key doesn’t display the key in the form or remove the form. Adding the key through the normal UI reports that it is valid and when refreshed says it is empty.
However, from the code and the ticket @eduardo mentioned, it seems the problem is UI based and that Akismet should still function (Only a guess)with a hard coded key (Can’t say about the key being stored in the database option though).
FYI this is also happening in non-MU installs.