For example, when I run the Super Street Fighter IV: 3D Edition on my 3DS, it just seems, very barely, to run slower than the cartridge version I own. However, I have no way of testing out the framerate of each game, and can only guess from my own eyes.
Is this true for other games? For example, with Super Smash Bros. already out on the 3DS (Japanese consoles only), would it run slower if I had gotten the digital version (9k blocks) or does my physical cartridge work faster?
Loading from an SD card versus a cartridge may affect the game's load time, the actual framerate should be consistent once the game is loaded into memory.
Having said that, SD cards are Flash memory and are relatively fast, so you shouldn't see an appreciable difference in load time either.
While this answer was based on my experience, comments on Reddit seem to imply the speeds are roughly the same or slightly faster if you're using a better SD card.
I believe that most games are either designed slow or the game creator wasn't thinking things through the right way. It all depends on the game itself. Physical games and downloadable games have no difference in frame style unless it is a bug that needs to be patched.
