I think that's only for the CycloDS(?)'s Clean Mode that you can't use cheats.
I turned on Anti-AP in Phantom Hourglass and was still able to use the Invisible/Visible Link codes. Also tried with Super Scribblenauts and they worked with Anti-AP.
Both games don't NEED Anti-AP, but I think if it's on then it's on.
I Put a Clean install OF AKAIO 1.8.1 with The Latest usrcheat.dat off of the Cheat database (Both which i already had) and I Have Had No Difference ( Also I didnt have AP fix on but i disabled it and still no difference)
If Anyone Has Got Some More Suggestions I Would Be Grateful,