The header situation is not normally an issue, when you know what's going on inside.
SNES headers are totally pointless, modern emulators ignore them, but the problem is that if you use an unheadered patch on a headered ROM, every byte change will be $200 bytes out of place. Simply put, just make a copy of your ROM and patch it. If the game crashes or otherwise looks wrong as soon as you start it, you have a header problem (assuming you picked the correct ROM revision in the first place). Mauron mentioned a tool in the site database that adds and removes SNES headers, but you can just open the ROM in a hex editor and insert $200 bytes at the beginning, patch it, then delete those $200 bytes, and everything will be fine. You can make two copies, with and without, and patch both. One must work, surely.
I should point out that I'm talking about SMC headers, which were added by ROM dumpers, and not the actual SNES header, which every game has, and is semi=important.