Okay, I managed with it. There is solution that working for changing size of objects that work very closely with physics
My final solution:
First of all it's need to separate collision shapes by roles(for default state, ducking etc) and switch them by $CollisionShape2DThatWeNeedToDisable.disabled=true
one and $CollisionShape2DThatWeNeedToEnable.disabled=false
another.
(Also I advice to change visible-parameter - it's good for further debugging things)
I made that, though now I think it's not necessary(but it's, as said cybereality: "using separate objects is easier for development and debugging"). In contrast with next point...
You absolutely can't change scale of collision shape, it's mess up physics engine to hell! You better to change position, rotation, especially shape parameters(image below), but only not scale.
That's all. Thank's to xyz and cybereality for advice all things that contained in this post.