I worked at an "Exhaust Pros" shop from 95 to 01. Putting weep holes in the back of mufflers was common practice. It helps the most on vehicles that have the muffler at the back of the car. In those situations the muffler rarely gets hot enough for the water to burn off.

On a regular parts store muffler, you don't have to get out a drill. We just used an "al" and punched the hole. If you are using a stronger muffler like a Flowmaster, the case is too thick and you have to use a drill.