A couple of ideas on why this might have been:
1. He knows too much. As things turned out, Kellhus' experiments with the Daimos ended up being pretty important to the story. So providing his perspective might have been too much a tip of the hat.
2. Optics. Of all Kellhus' atrocities, none were more concerning to his flock than his experiments with the Daimos. The Decapitants in particular were hard to square with his role as Prophet. So it might have made sense to keep Iyokus at arms' length.
Yeah I think your second point can work for sure, at least to explain his lack of presence during the strategy and councils and so forth (interesting, for example, how Iyokus doesn't even show up for moments like when the Believer-Kings gather or the Last Whelming -- I can't think of any reason off-hand other than what you suggest that would make sense for that).
Your first point is something I always flip-flop on with RSB. On the one hand, it's definitely fairly clear when certain POVs are held off (like the lack of an Aurang POV in all of TAE aside from a few snippets in TUC, presumably in order to avoid mention of the Mutilated), but at the same time he seems to have not have much of a problem giving a POV with very "selective disclosure". Pretty much every Kellhus POV in TAE does this, for example -- despite seeing his inner thoughts, to the extent of literally glimpsing his experience in the Outside, we ultimately are left in the dark about a great number of Kellhus's decisions and his ultimate plans or goals. Obviously part of this is just to secure the sense of tension surrounding the character and the Ordeal and so forth, but I think it extends to other characters as well. Serwa, for example, almost certainly knows about things we "aren't supposed to know" but RSB just avoids that stuff (or consider that, throughout all of the Aurang POVs in PON, up to and including the moments when he first realizes an Anasurimbor has returned, never once does he ruminate upon the fact that Kellhus's ancestor Nau-Cayuti was the freakin' No-God -- I know Aurang nor the Consult in general don't seem to realize the significance of using an Anasurimbor for the Subject, but still).
I wouldn't quite call this stuff "cheating", but it definitely cuts pretty close at times.
At the end of the day though I get the sense there just may not have been enough to warrant an Iyokus POV in general, as the only relevance he might have had was possibly, as you say, off limits. I think I was just expecting him to have a slightly larger role given his importance in the first series (his role is still pretty damn big TAE, arguably even bigger, but clearly there are details about the metaphysics and the Daimos which RSB is keeping mysterious, or just hasn't figured out).