Here is what I have experienced with cia builds on an N3DS with a9lh:
For the most part, 2D games run pretty well. However, Castlevania SOTN actually runs slower than Resident Evil 2 for me. I think most of the slowdown has to do with backgrounds; what I mean by this is that the frames in areas like the library in SOTN drop to about 30 with OP suggested options, but the same settings will make RE2 run faster than usual in most areas (cinematics are an exception).
Games with a full 3D environment like Evo's Space Adventure (abysmally slow), Spyro and MGS run the slowest of all (probably a moot point). I should mention that Mech 2 runs above fullspeed ingame with OP options enabled. Essentially, pre-rendered backgrounds have less strain on emulation as opposed to 3D and parallax-heavy ones.