Did you enabled the Widescreen-Hack or a AR code that makes it 16:9? If using a AR-Code, make sure that the Widescreen-Hack is deactivated.
The Widescreen-Hack is just a hack that doesn't/can't disable culling (as it is done by the game) but ususally with AR-Codes they also correct the culling.
The Dolphin-Wiki has a AR-Code for making it 16:9: https://wiki.dolphin-emu.org/index.php?title=Skies_of_Arcadia_Legends
The Widescreen-Hack is just a hack that doesn't/can't disable culling (as it is done by the game) but ususally with AR-Codes they also correct the culling.
The Dolphin-Wiki has a AR-Code for making it 16:9: https://wiki.dolphin-emu.org/index.php?title=Skies_of_Arcadia_Legends