My best guess as to why they would do this is for the sake of simplicity. If a game has an in-game tutorial that teaches you what each button does or has an in-game button configuration menu, they want the buttons labelled in-game to match the physical labels for the buttons.

Doing this makes the most sense if you're going to have a one button configuration. Why didn't they have multiple like the Super GameBoy and GameBoy Player? Probably because when the DS runs GBA games, it no longer is treated as a DS, but instead a GBA. It's very likely that this was a technical limitation on Nintendo's part rather than a plot against gamers or that it simply wasn't deemed important enough to spend the time adding button configs.