All of my MTM shirts are made without pockets. If I'm going to spend a reasonable sum (over $100) on a dress shirt, it will be MTM. That being said, I have found a few very nice dress shirts (Ike Behar, Hickey Freeman, Neiman Marcus, etc.) at outlet shops that were too good of a deal to pass up (under $40).
I carefully removed the pockets and cannot tell that they were even there. First, the pocket must be removed when the shirt is new. If you have worn and/or laundered the shirt, the area behind the pocket will look different after the pocket is removed.
Second, remove the pocket, using an Xacto blade or similar thin, razor sharp blade. Be very careful, take your time and cut the threads, not the fabric. You will see the small stitch "holes" after removing the pocket. These are not exactly "holes" in the fabric, but where the needle separated the fabric weave. After laundering and ironing, the fabric will reshape and the "holes" will fill in.
I'm sure some of the shirt experts on this forum will be able to give you addition instructions.
Hope this helps,
AD