Probably a little late to answer... but here goes.
From what I can understand of the problem - here is what is going on.
WiiSX (and WiiSXR, the more relevant one) use the psx gameid as the first slot memory card name (the second slot is always slot2.mcd and is "global" - i.e. not limited to specific game). Gameshark v5 (and front action replay, and I'm sure others) does not have a gameid in the place WiiSX expects it (system.cnf) and so WiiSX names the memory card '.mcd'. Not ideal, but not a game-breaking bug.
The trouble comes from ANOTHER bug in WiiSX, which doesn't clear the old gameid before loading a new game. So if you load one game / iso with a gameid that is not blank, that game id will stay (and be used for the memory card name) in Gameshark v5. I have not been successful so far in making a wiisx bootable gameshark v5 with a non-null game id (it boots in pcsxr, just not wiisx - which I presume doesn't like the iso format).
Either be careful to always load gameshark v5 first so that ".mcd" is loaded, or always be mindful (or intentionally load the same iso first, with a gameid, before gameshark v5) what the gameid is, because that is the name of the memorycard file that will be loaded. You can rename/copy the ".mcd" to any other game id name without issue.