I guess I should be OK. I do have Space Harrier 3D on my 3DS (and yes in 3D) but why Sonic? They were available a couple times in the past on card and via download.
All of these games are not roms but re-worked and touched up versions. That sonic is a slightly different game than all of the other versions; that being said, I do not think it's enough to warrant the digital price tag, but I do think it's a nice bonus for a physical game.
In the case of Fantasy Zone, there are two "versions" one where they changed the game so dramatically they added a W. This is entirely speculative, but I think that's because the game is in ~16:9 while the original release was more or less 4:3. If I am right, that would have dramatic implications to the gameplay for a carousel style shooter like fantasy zone. These are modified releases and basically ports to 3DS not emulators running roms a la virtual console.