Headered SNES roms used to be the norm in the late 90's, since back then ROM copiers actually used them for something (storing ROM type, mapping etc.). So the rule of thumb is that if a patch is very old and there are no specific instructions, there's a good change it needs a headered ROM. This also applies to the early 00's.
Incidentally, I remember a tool which allowed you to tweak patches themselves to work with headerless ROMs, but can't find it at the moment.
Maybe this is the one? it worked for me in cases the patch asked for a headered rom, but I wanted to apply other patches that didn't and it became a real mess, so removing the header from the patches themselves was the only way to solve it.