That may be a better question posed to someone who regularly shorts thru IB. You have to remember that most all brokers consider all penny stocks non margineable, which may or may not prevent them from being borrowed, depending upon the broker.
As for a brokerage house shorting shares held in clients margin accounts? I can conceive of the possibility but you would have to ask the question of why. The relative dollar volume on pennies is small compared to the big boards. Traders at the large brokerage houses command big salaries and bonuses. These don't get paid shorting pennies, especially if one gets out of control like LEX* did.
Most brokers had simply allowed the trading of pennies for the commissions. Somebody was going to make them, why not them. They limit their risk by not allowing you to margin them.