It's a very wild guess. No one have access to MGS3D source code, it's impossible to debug 3DS games and I don't think Konami would make a statement claiming their software is slow so... Also, people have got to stop guessing at exactly which fps a game runs.
No offense or anything, but I'm not guessing at MGS3D's framerate at all. Digital Foundry did a direct feed framerate analysis of the game and clocked it with a piece of software for accuracy (they've done this with other games on consoles to compare multiplatform releases of Ninja Gaiden 3, Arkham City and Sonic Racing Transformed, perhaps more). It confirmed what most people already knew. Throughout the test, the game never breaks 20fps no matter the situation., that is its maximum framerate potential. You don't need access to the game's source to determine that it never breaks 20fps. Check it out for yourself-
And it's quite often that the game will drop well below 20fps, occasionally during that test the game drops to 18, 16, and sometimes even 14 frames per second. It tends to drop the worst during cutscenes but there are ingame parts that drop as badly too. And to top it all off, there are even choppier parts than the demo above is showing. The intro is particularly choppy, as well as cutscenes after these, and people have mentioned certain bosses dropping immensely lower than what is shown in the video above.
At least with Rayman 3D, there are some situations where the framerate does reach its intended 60fps. Or in the case of Kingdom Hearts 3D where it's clear that the game is intended to run at 30fps and can often reach that. So whenever they become choppy, you can still tell that they have the potential to run better than they do. With MGS3D however, it never goes above 20fps in any situation. The PS2 version clearly runs far smoother and more consistently, the HD Collection even more dramatically so (PS3 version apparently runs at 60fps from what i've heard).
I don't usually have a problem determining when a game is suffering from framerate issues. And I can tell when something is running at 20fps and not 30 (i'd also be able to spot if it ever DID reach 30 at any point).