The question has been asked before, and there may not be a code for deleting the savegames of the Japanese GBA Gradius.
However, it is possible with the necessary hardware, for instance with a flash advance adapter (used with those gba flash cards). You could plug in the cart and then format its saveram/eeprom. How bad do you want this done?
It's not super urgent, but the save data is what's been keeping me from playing and enjoying this game. I'll ask on a Japanese forum first though, maybe they know a code.
If you are feeling brave, you can yank the cart while it is saving. IIRC a method of forcing a save without playing until you get a high score is just going into the options menu and changing a few things and then cancelling out back to the title screen. I don't know exactly when the data gets written, but you can try it at various points.
I know it's not a GBA game but I've done it this way with Judgment Silversword...