There are as many magic ciphers as there are races of elves.
Agreed this is a good question if only from a theoretical point of view and gives us something to think about and discuss.
One for each spell does not make sense at least to me as then a caster would have to know every cipher needed for their class.
As someone stated one for each spell casting class means that for a scroll to be used by different classes it would have to have two ciphers, which does not make sense when the scroll is created as you would need someone from each class to be available to place the correct cipher.
The cipher for overlapping classes again seems strange meaning they all have to work together to come up with these.
o either the scroll cipher is only for the class that created it or as I would play it - doesn't matter because it is magic and its just works.
I'm not sure what you mean here. The way I imagine it, the ciphers were invented or discovered by individuals, and their use has been disseminated through time until we arrive at the present state of affairs. It makes sense to me that spellcasters that have different areas of expertise would have bodies of knowledge that are shared across disciplines, while others are passed down only through specific traditions.
You aren't wrong, I guess I just tend to think of a 'cipher' being intentionally obscure to hide something instead of more like music notation or math where it is written as clearly and concisely as can be for the idea being conveyed.
I voted "other", and I'm with Rossbert above. I think scrolls are written is a single magical language. Anyone with a familiarity with the language can read it, but you might not understand the concepts written.
For example, a wizard can tell that a cure wounds scroll is a healing magic, but they can't quite understand the fundamentals of manipulating body and spirit in such a delicate and combined way. Without that practical training, they might be able to read each and every sigil on the scroll - just as I could read every English word in an advanced discussion on quantum physics - but they're still not going to be able to summarize the document or form a conclusion.
There are 3. One for each "type" of magic. Conceivably, if you wish to divy them up further, 6 if wishing to use specific magical/magic-using "languages."
The Divine Magic Ciphers: Celestial or Fiendish. Available to Clerics and Paladins of an appropriate alignment, Bards of any alignment. Possibly Warlocks of the appropriate patron.
The Arcane Magic Ciphers: "Arcanic/Magespeak/whatever your setting's incantations use" or Draconic. Available to Wizards (including Eldritch Knights and Arcane Tricksters), Warlocks, Sorcerers, and Bards.
The Nature Magic Ciphers: SylvanFae/Elfish magic or Elemental magic. Available to Druids, Rangers, and Bards. Possibly Sorcerers of fae ancestry and/or Warlocks of fae patrons.
This is a cool way of categorizing magic, but I don't think it addresses the function of the mystical cipher as described in the spell scroll entry in the DMG. For example, if there are only one or two ciphers for divine magic, why can bards, clerics, and paladins all read, understand, and cast from a scroll of raise dead, while only bards and clerics can read, understand, and cast from a scroll of speak with dead, while only bards and paladins can read, understand, and cast from a scroll of heroism, and only clerics and paladins can read, understand, and cast from a scroll of dispel evil and good?