There seems to be a lot in your question. I will try my best to answer what I see, if I miss something, let me know ...
What are implication for Academia SE users of recent licence changes and moderators disatisfaction and revolt?
The license was changed from CC 3.0 to CC 4.0. There are some immediate effects of that as the terms of the licenses are different. There is also the issue that SE has now set a precedent of retroactively re-licensing our content. This has raised the question of what prevents them in the future of attempting to re-licensing our content under a more restrictive license. The effect on Academia.SE users of the moderator dissatisfaction and revolt is pretty limited. We are still handling flags and user issues in a timely manner.
Another one wrote A request for SE employees and CMs User Apparente was suspended That user was very nice and insightful, wonder what happened.
I requested something in that question for CMs. I doubt anything will come out of it. The linked user was not suspended on Academia.SE so there really is nothing anyone, but that user, can say.
Everything I read it seems like moderators knew from the start of this year that something is going wrong, however they proceed with election for new moderators.
There are lots of things wrong, but I am confident that if we could go back to the beginning of the year, or even prior to the election scheduling, that few moderators would have predicted things going as poorly as they have. No one was trying to mislead anyone.
When I asked one user why she didn't apply for a position, she told me that big troubles are coming, now I understand on what she implied, however, if you all knew that why moderators kept us in dark?
I have no idea what this user told you, but apart from things we are not allowed to tell you, we don't keep you in the dark. In general, the things we are not allowed to tell you are "relatively small" (like what an individual said or PII) or scheduled for a widespread announcement.
We as ordinary users how should react to these new changes on SE, are we somehow affected?
I think each user needs to decide how they feel about the changed in the ToS regarding the right to sue, the ads and the fingerprinting associated with them, the re-licensing, and the public slandering of an SE user/moderator.
are our identities and location sold to third parties now?
I am not aware of any public change to the policies regarding the use of our identities and location, but this is not something I have been following.
Also moderators that suspend their activities commented or implied that they will come back, so what is the issue than?
I don't understand this question at all.