1. Yes, OMR cash works. And bank cards are an option to pay too, at least cards with PINs. [I have OMR cash, but it’s not always easy to get outside of the region and some other places unless planning in advance. I don’t know if there is a currency exchange in the area between the arrival gates and passport control at MCT, as I don’t recall seeing any and wasn’t looking for any, but I think I saw an ATM machine or some other kiosk somewhere in the area facing the visa on arrivals counter or just nearby to it, and maybe it could have been a cash dispensing machine.]
2. There is a visa on arrivals counter (usually staffed by two people) where you pay and get the visa on arrival receipt/paper. This is in a relatively open area before heading to the passport control line area. There were 0-9 persons in line ahead at the visa on arrivals desk when we have been doing it this year at the new MCT airport, but we are so late to get to the passport control area and visa on arrivals area after landing — nothing to do with MCT/Oman in particular — that I can’t speak to what proportion of passengers on my flights were using visa on arrival. The passport control line processing took longer than the visa on arrival acquisition process even when there were no passengers ahead of us in line.
3. For us, just coming into MCT. Mainly coming in from DOH on QR, but not only. I don’t go to Salalah, but I would be surprised if it doesn’t have much the same kind of thing too given it gets some European charter tourist flights, including from some relatively poorer parts of the EU.

The new MCT airport seems to be the cleanest airport I’ve ever seen.