Deadly Simplicity rule doesn't work on weapons about pf2e HOT 5 CLOSED

It was also raised by #203 in 2020.

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That is correct handling of the feat in the system.
As you can see from the prerequisite it only works for simple weapons and unarmed attacks.
Not martial or advanced weapons.

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So are we supposed to manually modify the damage for all other weapons? (The first paragraph of the feat's description.)

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The "Simplicity" bit in the feature's name turns out to be crucial:

Prerequisites deity with a simple or unarmed attack favored weapon, trained with your deity's favored weapon

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Even the First Doctrine explicitly predicates it:

If your deity’s favored weapon is a simple weapon or an unarmed attack, you gain the Deadly Simplicity cleric feat (page 113).

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