Do Gamecubes (DOL-001) without Digital AV exist?
Solution 1:
GameCube DOL-101 only had analog AV out
GameCube DOL-001 has both analog AV out and digital AV out
Which makes me believe your GameCube has been altered or repaired in some way with improper parts, it could be as simple as the back plate with the sticker being replaced because it was cracked
Source: