> Wait, each ship works completely different from the other ships, there are no established generic procedures, the crew just figures out how they want to do encryption?
There's some commonality, but it's like a fork of other ships. When a new ship is stood up and built, the pre-comissioning crew will write the SOPs for the new ship. Most of the time, you crib it from an old ship and make changes you think are useful, like a fork. There are some standards from up high, especially encryption stuff, but things can be run with some discretion.
Crypto was probably a bad example, since no decent Navy crypto tech would deviate from the proper procedures, even in the face of the CO asking for it. Kinda like how once the CO asked me to use more ordnance for training than I was alloted, and I said "no" and he said "yes" and I said "if you do this, I will put in writing that I told you not to and you did it anyways and I also won't operate the system to check out the ordnance, so we'll have an imbalance" and he said "ok".
> When you transfer onto another ship, do you need a long onboarding as well,
Not long, but a bit, yes. Much like starting a new job. For some jobs, you shadow the current position holder for a good while.
> does each ship have its own culture?
Yes, undoubtedly.
> How do they coordinate?
Generally via SIPRchat, radio, flag signals, etc.
But seriously, we have some standards for operations that make the different ships able to inter-operate easily. You also have groups of ships under commanders who do a bit more to coalesce those ships into a unit.