Why hasn’t Dwolla been incorporated into invoicing software or applications?

Hard to say, though it would be a great thing if they did. Many people in the field still feel Dwolla is still very nascent/new. Invoice companies like FreshBooks, BillGrid, et. al., all are probably keeping an eye out on Dwolla. They wouldn't want to risk spending too much time and money on integrating Dwolla only to find out that company goes bust (or changes direction).

My bet is that none of the Invoicing companies are will to take the leap-of-faith with Dwolla, not yet. Maybe in the coming months. Dwolla's main stream penetration is still very light, even amongst the Freelancers, Dwolla is not known by everyone, let along used by them.

You may just see a domino effect, if say FreshBooks were to integrate Dwolla, others would very easily follow suit.