The enemies are moving by some force, right? You'll be using a float for speed most likely.
They must have some sort of even rudimentary AI system in order to operate, right? There must be at the bare minimum something that will move the enemy in a direction, and you'll need a float or int to control the speed.
When the enemy spawns he has to use some float variable to start moving, right? Speed. When he spawns, before he does anything, just force him to get a new speed variable from some game object/script/fsm in the scene.
You can change that Speed variable at any time, right? Just change it at the start of every wave, then any enemies that spawn will grab that new speed and use it. It's the same variable, you just increased it, hence making them move faster.
You could do this easier with global variables, but in my experience they are clunky to work with..