Your approach has two flaws:
It cannot scale down to 0 polygons effectively when they are connected to each other.
In order to do that you need to know exactly how much far away each point is from the center of mass so you can enter half of that as a value to the Plain Effector. In your scene if you hit render you can still see the scaled-down polygons. Estimating this value is very hard
2. Your second tube was neither round or straight as the first one. This is a serious difference from the first object. A polygon or point can be manipulated relative -to many things. Usually they scale relative to their normals. You set polygons to move towards the Z-axis by a certain value. So the affected polygons (that also are connected to each other) move towards the center because their normals point to the center due to their arrangement (circular). In order to both move and stay connected to each other they squiz themselves before reaching their destination. So scaling was a by-product in your case.
You should be scaling their points.
Now moving to the hexagonal tube, each polygon's normal did not point towards the center. Flat surfaces of many polygons point collectively to the same direction. That's why you witness that weird brake on the corners when trying to move them along their local Z-axis (normal axis).
As mentioned before polygons can be scaled relative to many things. If your object does not have a common center to scale down towards along all of its mass the trick by providing a single value won't work. So you can try to make the polygons scale relative to something else. This time the Effector itself (pivot point). do that just change the Deformation to Point, Transform Mode to Absolute and Transform Space to Effector. Move the Effector itself in the middle along any point of the object and also move the Timeline. You will notice that the object vanishes by scaling down but it does so ineffectively. The reason is this:
a. The effector is stationary. As the Field passes through so must do the Effector. So every point wants to scale (points do not actually scale) towards the effectors position.
b. the object gets deformed in many unwanted ways. This is because the polygons are connected and want to remain like so.
So an Effector is not a good way to "vanish" an object in the way you'd like to (by warping it like if it was sucked by a wormhole).
The only way I've seen Effectors to make objects disappear is with the use of the PolyFX.
PolyFX will disconnect all polygons so other Effectors can manipulate them discretely. In your case scale them to 0.
The problem with that is obvious: Your mesh will break up, even with Fields disjoining polygons at the latest of stages will most of the times not be a plesant visual effect.
None of the above is a problem with a deformer. A deformer will move each point of a mesh according to a differential space formula. So essentially we still have a scaling of polygons as a by-product but it's not that obvious because we don't explicitly deal with movement, scaling or rotation.