"default-emotop" is the name of a template. It's the old v3 default template which puts emoticons along the top, hence the 'emotop' name.
I never saw JoComment 3 (i went straight to 4 when I joined here) but I assume some things between 3 and 4 were just renamed.
Is there an upgrade guide Daniel? I thought there was. Well if there is, it should definately mention an instruction to go into Settings and Save Configuration after upgrading, if it doesn't already. So it's not really a bug, but a good FYI