Zion:
After imprinting in Zion (which excluded Warlord’s plot), what should I do next to continue their storyline? Am I supposed to something special in DeepMines? I’ve been in DeepMines, only finding entrance back to Factory. Am I missing something or not supposed to go in DeepMines? Where should the code \\ZION be used? Did using O8’s code make or break story progression? How to use Self-destruct Interrupter?
Are you referring to the Mines branch found in Materials? If so, there's nothing special in terms of unlocking plot-related lore, although you might find some interesting stuff there.
As for \\ZION hack, the derelicts said to use it at a terminal. However, that would mean you'll have to go back to the Factory floor. Once you find a terminal, the effect will become apparent.
The self-destruct interrupter is something that will....you know, interrupts stuff from self-destructing. It's something you're supposed to figure out yourself. But here's a hint: What is the one thing that self-destructs? ;)
DataMiner:
Does DataMiner has a storyline? Where should the GodMode code be used? In Warlord’s base, Research or somewhere else? Is the code \\IAMDERELICT merely provide alternated exit?
Since you've met Warlord, you've probably figured out that the God Mode hack is not to be used there. As Warlord mentioned, that was a fake one. Where else could God Mode be located? It should be pretty obvious if you've met Warlord at Research.
The \\IAMDERELICT code is an alternative exit at Storage, which would lead you to a new branch. Go there to find out.
Zhirov:
Zhirov’s terminal mentioned three things, Sigix pod, SGEMP and ArmoryLab. It seems the seed is preventing me to do all three in one go. Which route should I take to do all three? If I’m not supposed to, which one is needed to progress Zhirov story? If I bring SGEMP to Access, Zhirov would appear on Access but warp out on Command. What should I do next?
There is a way to do all three of these in one run, but it's seed-dependent. If you want to be certain, find out which seed allows you to do all these 3 quests and then record them.
Others:
Is Hub_04(d) merely score attack? or necessary in fighting MAIN.C?
Does Query() affect map generation?
What to do with Signal Generator?
Where can I find the Zio. line of weapon?
Does blowing up cooling machine on some floor serve story wise purpose or just a floor only evacuation mechanics.
Hub has something special in there. Go reread your Oracle records in your lore collection.
Query() is just for obtaining lore, so it has no affect on anything.
Signal Generator is for......generating signal. I'm not sure if it has any good use, but one of the derelicts said it could be used to derail assault squad.
Blowing up certain machines do trigger certain stuff. Usually they are colored cyan. I don't think blowing up cooling machines have any effect.