So, basically, I launch the Classicube via homebrew launcher, I can sign in, fiddle with options, but if I press Resume, Singleplayer or Direct Connection/Multiplayer, my 3DS just crashes. Even if I don't sign in, it still crashes. Is there any way to deal with this issue?

The same thing is happening to me

Did you try using the cia version and not the 3dsx, because the cia version works fine for me~