If you are installing an aftermarket in-dash unit similar to the OEM unit, yes, you'll need it flashed, and it would be helpful to have them also unlock all the towing screens in your EVIC. A word of caution, some of the aftermarket units don't work well, so a lot of guys who go that route just go with the OEM unit.
If you're getting something like a P2, no, you don't have to have the computer flashed, but the control isn't as seamless as the OEM in-dash unit that actually proportions brake application on your trailer by monitoring the input on the truck. It's good, but not as good.