Honestly, I'm pretty sure a spell with a DD and secondary effect would just make its resist check against the secondary effect. This would make enchanter nukes easier to resist since it's easier to resist a stun than it is to fully resist a nuke. It wouldn't be relevant for druid roots and shaman dots because it checks for the root and dot component, and those are as easy to resist as any other similar spell without a resist modifier. There should be no saving throw against the DD component at all, hence why it can't roll for partial damage. So:
Enchanter nukes: saving throw vs. stun, thus easier to resist than other nukes where there's a roll for partial damage. Enchanter nukes (and certain wizard/druid nukes, as well as the cleric stuns that do damage) can't do partial damage and will always do full or no damage.
Poison/disease dots: saving throw vs. dot, thus the same chance to resist as any other dot except the ones with resist modifiers.
Druid/ranger roots: saving throw vs. root, thus the same chance to resist as any other root. I believe there was a while where the DD part could break the root instantly, however. This was then fixed by making the DD apply before the root effect. Not sure when this happened.
That's how I remember it, and it's what makes the most sense. It's absurd to assume that these spells were twice as easy to resist.
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