Usually, there are about 512 bytes at the begining of a SNES rom dump that are not part of the actual game. It can be safely taken out, and the major bonus is that the rom is easier to work with since you won't need to be adding +200h to every offset. The downside is that what gets created in a headered rom requires a headered rom to be patched, and some people are very anti-header.
I am one of those people. Headers, essentially, contain a little bit of extra data appended by copier devices (such as a Super Wildcard, Super UFO, or Game Doctor SF). This little bit of data differs from copier to copier but typically contains the same information - sram size, number of banks, that sort of thing. It mainly functioned an obfuscation device so once ROMs were inevitably dumped and passed around they wouldn't work on a rival's copier device.
As stated, headers are not part of the original game: they're data added by copiers, and they tend to make address calculation a pain as every string or ASM command appears 512 bytes after the address it's supposed to be at. There's no really good reason to keep them attached to a ROM, excepting the fact that a few ROM-editing utilities inexplicably require them. This makes no sense to me as not only is address calculation made more difficult, but headers are copier-specific: a ROM with a header will work on exactly one type of copier, and there are easily half a dozen different brands out there. Chances are the header's not going to work on your copier if you have one, and you're going to have to use a utility (such as inSNESt) to convert the header (or add one back) regardless of the header's current presence.
In short, headers are like tonsils: they serve no practical function for most users and cause more problems than they solve. They're vestigial and ought to be removed before any work or distribution is done.