Is it worth upgrading my wheels on a commuter?
Yes, I think it's totally worth it.  It depends on if you have a budget to spend on extra parts of course.

I have a specialized secteur as my commuter and after a year or so of owning it I replaced the stock wheels with some mavic aksium wheels.  Now, the decision was made as part of a groupset upgrade.  The bike was equipped with a low end shimano 8 speed and I got the wheels as part of an upgrade to an 11 speed groupset.  That said, the wheels are on the low end of an aftermarket wheel and they still make a huge difference.  They ride much better than the stock wheels, are lighter (but still heavy by road/race standards), more responsive, and brake better.  

I also bought some locking skewers with them and don't ever worry about carrying an extra cable or anything besides a good lock.  The downside is that you need to carry your skewer key around everywhere, but I usually just keep mine in my bag.

Of course, they might get stolen, or your whole bike might get stolen because it draws more attention, but if it's something you want to do and aren't going to be upset if it happens, don't think twice about it.  Make the upgrade.  I'd recommend getting a used wheelset.