While they do function on a higher level than the heartless, thought on the level of sentience doesn't occur. Only thought on a sentient level would result in "rebellious behavior" like that of not following the organization.
As far as the Dusk speaking "We have come for you my liege" line, this shows that Dusks are capable of speech, but it doesn't show that they have a high level of intellegence... It would be simple enough to have a Parrot relay a message right? I'm guessing it's a similar case for the Nobodies (though they're obviously more capable than parrots). Basically a Dusk could be ordered to let Roxas know that they came for him, speak the line, then do what it took to do so.
You're pulling this from absolutely nowhere.
Yensid states that Nobodies are capable of thinking and planning, and he never specifies further than that. He meant Nobodies in general. Planning and language require a higher level of thought because they deal with the abstract and hypothetical. Even if just in one instance, a regular Nobody was shown to be capable of speech, and you have no actual reason to believe that this was just "parroting."
Nobodies don't lose their minds, why would they lose its function? Perhaps to some degree they're impaired but not on the level you're suggesting.
With that in mind, it's difficult to see why the Nobodies would follow neo-Organization XIII. They must have been aware of the end goal of the Organization, from which they'd directly benefit. And when they realize this was a lie, and the actual purpose is for reigniting a war that they have no part in, then they'd rationally want nothing to do with it.
Even so, I'm sure they'll end up being enemies anyway. Either they'll come up with some explanation (like mind control or a new objective) or just forget to offer an explanation altogether and not actually think things through.