Hi
I think the most popular approach in thickness measurment is ULTRASOUND.
As you know the exact metal that used in the pipe, you can find the sound speed in that metal and with a simple physical relation(velocity=distance/time) you find the thickness.
The problem that may occure is that sound can't travel in the air. Maybe you have to fill the pipe with water.But it can be helpfull in your case, beacause hole in the metal is like a air bubble and it's very easy to find this holes with ultrasound.