Beastiary 1 p 342 describes Covens and lists spells they can cast.
Click for Coven description.
1. Since Covens may consist of monsters of different levels and abilities, how do you determine the spell DC for these spells? It does not call them Innate spells.
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After the coven is formed, each of its members gains elite adjustments, adjusting their levels accordingly.
Click for Elite adjustment description.
Increase the creature’s AC, attack modifiers, DCs, saving throws, Perception, and skill modifiers by 2.
2. Also, since a Coven increases DC's for all members by +2 due to becoming Elite, would that also increase the DC's of the Coven spells?
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All covens grant the 8th-level baleful polymorph spell and all the following spells, which the coven can cast at any level up to 5th: augury, charm, clairaudience, clairvoyance, dream message, illusory disguise, illusory scene, prying eye, and talking corpse. Individual creatures with the coven ability also grant additional spells to any coven they join.
3. When it says 8th-level Baleful Polymorph (a 6th-level spell), does that mean it's heightened to an 8th-level spell?
4. If a Coven made up of level 3 creatures cast Charm could it still be cast as a 5th-level spell? Could they cast that Baleful Polymorph as well?
I've actually thought over this quite a bit:
1: (This is a personal interpretation) I would call the DC of the coven spell as being equal to the spell DC of the coven member that actually took the actions to Cast the Spell (not just the single action to contribute to the coven).
2: If the coven member was elite then all their DCs would go up, which would include the "primary caster's" spell DC (see above).
3: Yes.
4: By the RAW: yes. They are essentially pooling their resources together to cast a spell that the individual coven members could not hope to cast. Though I do admit, if those spells go off it'll suck for the low-ish level party that has to try to get rid of it.