I second what all of these guys said. Take a board with 100 components, pretty simple. Loading it up on a pick-and-place machine with all SMD parts takes an hour or two. Having the machine place 100 parts is going to take about 10 minutes (and that's a really slow machine, placing only 10 parts per minute). Reflow, and boards are done in a total of a couple of hours.
Now take a through-hole board. Not only does each part have to be manually soldered (or manually tacked then wave/selective soldered), but prior to insertion, each lead needs to be bent at a 90° angle. After installation, each lead needs to be clipped to flush (or almost flush) with the board. It's really time consuming, and you will pay for it in assembly charges.
The only justification I would have for designing a through-hole board is if I only planned on building one and had no future use for it. Other than that, SMD is the only way to go!