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If you mean the junction box puzzles, they're not for codes, they unlock doors/buttons. I believe most aren't required, they're typically just the shortest route to an important area. There are some required ones, including the ones in the final level, but you could probably logic probe all the required ones to skip them.
Pckables: I have not had any problem with the box puzzles, they feel like a pipeline/flow game.
Cyberspace leading to a code only occurs once; on Research. In pretty much all of the other cases, the cyberspace locks are just for doors. Some of them are mandatory, others may provide a shortcut or open a side room.
It's safe to not ever go into cyberspace, except in order to complete a handful of specific objectives, and you should be able to find clues as to which ones.
Every floor (except the groves) has a Cyberspace Terminal. I don't know how many are optional, but off the top of my head, I'm fairly certain the ones on Research, Executive, and Engineering level are required.
Executive - not mandatory, there's an alternate solution
So apart from that...
Engineering... can't remember, probably mandatory..?
Maintenance - mandatory
Research - mandatory
Medical - mandatory
And that's it, everything else is optional.
Light Spoilers below:(lvls not mentioned have no cyber sections)I list them in order of lvl.
Reactor:cyber 1: afaik optional opens up armory for loot.
Medical
cyber 1: optional but opens the armory for early magpulse+loot.
cyber 2: Mandatory to disable progress block.
Research:
cyber 1: in the libary mandatory for the laser code:(very hard section).
cyber 2:Optional purges most of the radiation around the the X-22 area.
Maintaince:
Cyber 1:needed to access CPU node core,if only 1 digit is missing you can still quess the 6 digit code so this is semi mandatory but very recommended to do for the whole 6 digits later on.
You will only access cyber once the maintaince lvl opens up more as story progresses.
Flight deck:
Cyber 1:afaik it is optional it opens up an armory and maybe some other doors.
Executive:
cyber 1:Can open a storage room and the beta grove: afaik optional.
Beta grove can also be opened from the hidden office same place from the prologue.
System Engineering:
Mandatory and very long:
It has 4 nodes to destory to unlock 4 mandatory places.
VERY easy to get lost.
Security:Optional unlocks an optional place for extra fight,loot and audio logs.
Bridge:Mandatory:Different rules apply.