The question that comes to mind when I compare commlinks to cyberdecks isn't "why can't commlinks run common cyberprograms?"...
Instead, I ask, "Why do all deckers have to be rich?"
Better hardware gives an incentive to upgrade, of course. But even the wimpiest, bottom of the line cyberdeck costs 50k, and a passable midrange deck (the Microtronica Azteca 200) costs more than a permanent Low lifestyle. That's before you buy a datajack, programs, various other cyberware or bioware that enhances your hacking skills, etc.
It's a strange disconnect, because I find it hard to believe there are that many SINless folks out there that have the resources to own a piece of hardware that costs more than a house. Not to mention that that hardware is highly illegal, and incredibly fragile. One bad run, and your deck is locked away in a Lone Star evidence room or fried from enemy IC. Your standard gunbunny can lose all of his equipment and buy the minimum he needs to function for a few thousand nuyen. Even riggers have an easier time replacing equipment than deckers. It's one of the few things I didn't like about 5th edition. 4th may have made decking equipment too cheap, but I think 5th went too far in the other direction.