Using this setup in animation nodes I created a phantom effect for my text with a wave modifier, but when I apply a boolean modifier it gets rid of the transparency of my text. Is there a way to apply the boolean without effecting the text transparency?
You are storing your transparency information in vertex colors layers. Some modifiers—including the boolean modifier—are destructive when it comes to mesh data such as vertex color layers. So upon applying a boolean modifier carrying vertex color data, the data is destroyed.
You have two ways to fix this, you either use another medium to pass the transparency information to cycles, or you dispense the boolean modifier in favour of another approach to achieve the same effect.
Dispense The Boolean Modifier
A more efficient approach would be to write a shader that changes the transparency of the fragments dynamically. Use the object space texture coordinates of an empty as the vector input of a Quadratic Sphere Gradient node and get the fragments that their gradient value is larger than zero. Use the output as a transparency mask and animate the empty location and scale to get the effect you had before: