Like Special Guests, filk guests at conventions are sometimes a Guest of Honor position and sometimes not. There is no easy way to tell — you just have to read what the convention's publications say and look at the convention's practices.
Conventions sometimes have "Music Guests". This is probably most commonly a filk guest. (In some cases the convention thinks that calling it "filk" is somehow demeaning, perhaps similar to how some conventions call hucksters "dealers".) But sometimes a Music GoH is a guest who is simply a mundane musician that the committee likes.