The instruments do exactly as you say (run the sample N times), but this obviously comes at a cost. Also, keep in mind that sequencing needs to be very, very accurate to be useful. We share most of our DNA, and the small variations make up all the difference.
Yes, those are all relevant costs. There's also a tradeoff between accuracy and the number of reads (how many sequences you can observe), or how much data you can get out of the machine.
