It's very common on business servers and security/gateway appliances for load balancing and contingency, a (workstation) mobo with 2 network ports can be handy in some situations if you have multiple networks connected up and you want a PC to sit between the two as a form of controlled switch/bridge.
I would guess they considered the P5Q Deluxe to be high end/performance/workstation class stuff when it was released so pack as much functionality onto it as possible and charge a higher margin for it was probably their thinking behind it.
Lots of flashing lights and big cool shiny stuff = Interested Customer.
One gigabit port is sufficently fast enough for the majority of us, in fact without the necessary supporting (gigabit capable) hardware infrastructure, you'll most likely never hit anywhere near the throughput speeds that nic can offer.