Here's how your sentences read to me:
1) It has been deactivated (by someone/something else).
The 'it' is passive, and has to be acted upon. That's what the 'been' seems to imply here.
2) It has deactivated (by itself).
No one did anything; the machine or device or whatever had an "automatic off" program and turned off.
Think of a microwave. You punch in 30 seconds, it runs, and then it shuts off/deactivates. But, if your food starts popping and splattering all over the place after 20 seconds, you open the door and deactivate it yourself. The microwave has been deactivated.
As far as the ongoing process that you mentioned at the end of your note, neither is totally clear on whether the process could start up again. Both could work. "It has been deactivated (but can be reactivated if we want)." "It has deactivated (for the time-being, but will reactivate in the morning)." Again, I'd say here the underlying idea is the independence of the whatever "it" is standing in for. The first sentence implies someone needs to go in and reactivate; the second sounds like if "it" starts up again, it will be of its own action.
So, rather than time, 'been' here has more to do with voice, passive versus active.