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When are pregame stratagems used?

In particular those that enhans models, like ekstra relic or warlordtrait. Or making some orks ardboys. I do not know if there are any difference between the wording of 9th edition codexes like SM, and 8th edition codexes like orks.

What about those that gives deep strike or other such things? And how do they work with units that can combat squad. (Outflanking (SW) some combat squaded group for instance.)

Pregame stratagems that change units in any way are used when you write your list.

Those that modify how a unit is deployed, it depends on the specific stratagems, but tipically they would be used on step 10 of the pre-game sequence, after determining attacker/defender and choosing deployment zones but before you start deploying.

So I could not say use the 'get an ekstra relic' after I know what opponent I am playing? Do you know where it is stated?

No, you cannot. That stratagem must be used in the Muster Army phase of a game, which is simultaneous for both players.

Under the Battle-Forged Army Roster section:

"If a unit has been upgraded by a Stratagem before the battle, your army roster must make a note of the upgrade (e.g. Stratagems that enable additional models to have Relics or Warlord Traits or Stratagems that grant units better characteristics or abilities). If a unit has a Warlord Trait via such a Stratagem, these must be noted on your army roster."