I'd reccomend doing it in a vertex shader to not destroy performance by either always having that many meshes loaded or creating a lag spike on death (by having to create as many meshes as vertices). This is because Godot is fairly high level, so all of its inherit classes have some overhead, and when used (abused?) to this degree it becomes noticeable.

You'd have to know some vector math to make it customisable, but for the flame one I'd take each vertex move it down x units each timestep, clamped to the floor's height

Edit to include an exploding example I made elsewhere in the post

void vertex(){
    VERTEX += NORMAL * (sin(TIME)+1.0) *0.1;
}

Godot does have a special thing for mesh instancing, I think variations were possible as well like different colored triangles maybe? https://docs.godotengine.org/en/stable/tutorials/performance/vertex_animation/animating_thousands_of_fish.html

Assemble your objects from smaller, independent 3D meshes, which you can control separately after destroying an enemy. That's how I do it in my space shooter game.

Create meshes that are separated into different models to do that. That's how I'd do it anyway.

1 sounds like it could be done with a shader, 2 would be an animation. Could probably also do 1 as an animation (here it a way to do it in Blender)