So does the new version of Fey Wanderer makes it so you can't use the extra 1d4 damage with two weapons like dual crossbows?

Dreadful Strikes

3rd-level Fey Wanderer feature

You can augment your weapon strikes with mind-scarring magic, drawn from the gloomy hollows of the Feywild. When you hit a creature with a weapon, you can deal an extra 1d4 psychic damage to the target, which can take this extra damage only once per turn.

You can use it with two weapons, you just can only apply it to one hit per enemy per round.

So you cant hit it twice on the same enemy, even if its with two separate weapons?

Quote from frozenmaw >>

So you cant hit it twice on the same enemy, even if its with two separate weapons?

Correct.

Notice that it specifies that the creature can only take the extra damage once per round.  Meaning that it does not say that you can only inflict the damage once per round.  So if you attack multiple opponents you can deal the extra damage to each of them.