The mod installed early game, enables Logistic Tab, which really could not yet be available on current tech level.

The logistic slots are used to customize the inventory cleanup hotkey, so they have to be available from the start. If you disable the hotkey in map settings, it wont show the tab until its researched.

Was it always work that way?
Maybe there is some "default" settings for Ctrl+C that could be used, until logistic slots are researched?

What is always work that way?

Yes. There is an internal default config, but without the slots you cant customize it. And since the hotkey is mostly useful in the early game before you have bots, that would be very annoying.

The logistic slots dont really do anything until you have bots, so I dont see a problem with enabling them. But if you really dont want to see them, there is a setting in base factorio (Interface > Flat character GUI) which hides the logistic slots under a separate tab...