uh I guess minor spoiler from past stuff.
as Itsara said, the nameless himself said he is not the culprit behind the shapeshifters or the chaos in northcrest, so I seriously doubt he did it. I only trust him since so far, he hasn't lied to us, just hid things he doesn't care to tell us. plus, we find out it wasn't a living person/beings influence that made the shifters, but a relic that someone else found giving more credence to nameless telling the truth. also, we don't even know if the shapeshifters are aware the nameless exists like he is aware of them which would further disprove the idea he is involved. and again, he warned us of the shapeshifters knowing we were getting involved with it to try and stop them, so if he was involved, why warn us? we completely destroyed his corruption of the lizard tribe plan so he would prolly want to keep us away from northcrest if he was in control or going for control, not warn us of the danger and leave us be.
(And another small detail that isn't really stated anywhere so it's mostly speculation on my part, but I think the nameless isn't supposed to be EXACTLY like Cthulhu, just similar designed and some other similar character traits.)
so like TLDR, in my opinion no. it would make literally no sense if nameless was the one behind the shapeshifters based off everything about him so far, so our tentacle husbando is safe for now :)