I made two questions a couple hours ago and was downvoted by some users (even if one of them received enough upvotes to return to 0). When I asked why some people said that lore questions (about games, of course) are not welcome here by some other users. Is it true? Please help me to become a better collaborator of the site. I don't want to keep asking things that are not allowed. Thank you all in advance.
The first thing to note is that we don't all agree here. Lore questions are allowed, but some people disagree with that. More specifically in regards to your question, some people think that lore questions are bad and downvote them.
Another problem, as fbueckert pointed out, is that your question basically describes a hole in the plot of the game and asks for a resolution (hence "poke the plot hole"). The most likely answer is that the writers didn't think of it, which means that your question is likely unanswerable. This probably led some people to vote it down.
As far as I know, lore questions are perfectly fine.
You do have to ask constructive questions that can be sourced (either by external official sources, or in-game content).
Your questions seem to solicit discussion:
Did Morpheus suffer any consequences for his actions?
What was Hades doing by the time Atlas was destroying the Pillar of the World?
Lore questions are definitely allowed based on our current guidelines. But allowed does not necessarily mean universally liked.
Voting (both down and up) is the community's way of deciding how useful a question is. It is very common for questions to get both up and down votes, as some members of the community will find a question useful, and others will not. Downvotes have less reputation impact than upvotes, so even if every question you ask got the same number of up and down votes, you'd still end up gaining rep.
There are a number of users in the community that find many story/lore questions to not be useful. That's fine. As long as you ask questions that are useful to at least some of the community, you're in good shape.