CMP #$00 always set the C flag, and SEC is more efficient in doing so.
AFAIK it is wrong to expect that Squaresoft's games are all masterly programmed (just because they are masterly concepted)
Well, this is interesting, I never thought of it this way, but I think you're right. Some shitty games could have been masterfully programmed and vice-versa.
At least I know some early NES Square games have really stranges programming quicks and are programmed in a very non-standard way for the console (i.e. the games don't use "true" interrupts, sprites have hard-wired OAM positions and the engine relying on them, stuff like that).