The short answer is no. There's no 3D* and the game has no major changes.
However, there are a few minor tweaks to non-gameplay elements:
- Grandma Ulrira no longer has her "YAHOO!" shout; it's been replaced with "HELLO!" and "YIPPEE!".
- Effects that make the screen flash (e.g., capacity upgrades) have been slowed down greatly, like most other Virtual Console games.
- Mamu's song loses the spotlights, which were done by rapidly flashing parts of the screen
- The photobook no longer allows you to print pictures. The game ignores the A button entirely, so you can't even get the "Error 02" message.
- Inaccurate emulation bugs sometimes lead to minor music and graphical inconsistencies
The actual changes to the game itself have been verified by examining the game's content. The ROM itself is a standard Link's Awakening ROM with an included text-based patch (applied in real-time).
* Holding Start or Select when starting the game will render the game at original size (no filtering) with a faux-Game Boy Color border around it. The game screen is slightly sunk into the border using 3D effects.