I'd say most of the companies that were in the WTC had disaster recovery in place for any critical equipment that was there. I'd expect there wasn't much of that. The WTC has been a terrorist target for a long time.
I work in the I/T outsourcing business and deal with many commercial accounts (but not at the WTC). My experience tells me that although residents of the towers suffered major losses and/or setbacks, that this should not suspend their core business from functioning. I have no proof, but, I'm fairly confident I'm correct. Only time will tell.
As for the loss of the communications tower at the top, I have no idea what kind of short or long term impact that'll have.