Flaks can still push away small ships the same way they used to. And they do also push away NPCs, if "push away" is the correct word. But I think "yeet" would be more fitting.
Basics Flaks also push away caps npc's, i've noticed that on missions. I still have the feeling that the EMP codes flaks push the caps away harder than the basics.
The EMPs blast doesn't have a stronger knock back effect, but the shells travel at a greater speed, so when that difference is added, in practice their knock back effect is stronger.