Effectively, I don't think there is any difference. But 'raised' is a very general adjective meaning 'above/higher than' (the pattern of the seal stands 'higher than' the surface it is printed on). But 'embossed' refers to the skill/craft of embossing, which is usually used when you talk about formal/official things. Very smart notepaper may have an embossed logo; posh wedding invitations may have embossed lettering; expensive leather goods may have embossed symbols/logos.
So it's a matter of context and connotation, really.
I believe a seal that is embossed must have been pressed out from the other side of the document to raise the pattern. A raised seal, on the other hand, could just be thick ink or paint on a flat surface or a sticker placed on top of the paper or document.