The header and footer files can be either text or html, it makes no difference. The header files go into the admin/header directory, the footer files go into the admin/footer directory.

If the header or footer is short, there is no real need to put them into a file. You can just store them in the field for the category record. When Links look at the field, it first tries to find a matching file name in the directory. If it does not find one, it will display whatever is in the field.

I hope this answers your questions.