-How 2B's(and to as lesser extent 9S) costume is in any way pratical for combat.
-Pretty much any of the costuming in general.
It's a fantasy sci-fi setting where they decided that unique character design was more fun and memorable than stark realism.
It's obviously a matter of personal preference, but it honestly doesn't bother me in the way that a design like Quiet's from MGSV would bother me. In Automata all the Yorha units match a general stylish aesthetic that doesn't make 2B feel grossly out of place compared to the rest of the main cast, while a character like Quiet is the only person wearing frilly underwear and torn tights in an army of gruff realistically dressed soldiers. It's kind of a lazy character design on MGS's part and just looks silly standing next to every other character.
But again, personal preferences.
-Why do they use operators in the bunker when interfacing directly with the bunkers comm system would be faster and involve fewer parts. Having an android standing there operating a console is completely inefficient. Ghost in the Shell actually brings up the same issue and at least there the answer is "So the humans feel more comfortable talking to a machine".
So the player and character could have a support specialist to talk to and exchange general information with?
-Why Android use beds, eat and take showers when they don't need sleep, food or comfort.
-Why does throttling kill an android when they don't need air(and can survive the vacuum of space just fine)?
They don't need things like food or real sleep, but they do it because they want to. Everything that's unnecessarily similar between androids, machines, and humanity is part of their desperate desire to emulate humans more closely.
2B even points out how things like that are inefficient, but 9S says it doesn't matter if it feels good.
What is the purpose of having an aircraft carrier when the android have flight units which appear to be able to go to and from orbit whenever they want and V/TOL capability to boot. Even as a missile ship it's way too big and costly for that role(Carriers have huge crew requirements).
The flight units are limited, and aren't really fit for carrying huge amounts of supplies. The overall android resistance is much larger and less advanced than just Yorha, which is basically a small special ops group, so I guess they make do.
Though I guess you could say it's just an excuse to have an ocean-based boss fight.
-How did emil find a working truck 9000 years in the future and how is he driving it?
Emil's an immortal magical being that existed way before the machine war ever started. All of his clones took on different roles at the start of the war with the aliens, and the one we meet was set up to carry supplies to and fro. But his role in the conflict, as well as a lot of his memories, have long since faded. So he re-purposed his cart to become a roaming vendor.
-How Yorha's battle strategy seems to devolve down to "Fly to the surface, kill robots" most of the time. Hell, the robot factory wasn't even taken out from the prologue, which seems like it would have been the point to that entire costly mission. There's some lip service to using S andriods to knock out the defenses before hand, but those just seem to be a prelude to "Land, Kill robots" as opposed to "blow up the infrastructure used to make more robots" or "Cut off the robots supply lines". It's basically the Starship Troopers movie all over again. No wonder this war has been going on for 6000 years nonstop.
The pointless battle of attrition is a big part of the theme and later plot revelations. The machines vastly outnumber the androids, and no matter how many of their facilities are destroyed more just keep cropping up.
I guess it could be a story about the androids endlessly carpet bombing the planet's surface, but there wouldn't be much of an Earth left to reclaim for humanity afterwards. Or much of a game to play.
And the fact that it is a game counts for a lot. Katanas sure as Hell aren't going to be more efficient than a tactical missile strike when fighting a giant robot, but whatever. It's fun.