It actually is cheaper to nightstop crew. I was told the figures a while ago from someone high up and I can assure you that based on Flybe's business model, it is cheaper to nightstop crew rather than have an operational base. Please bear in mind this is based on having less than the ideal 3 or 4 aircraft in base. Why do you think they closed GCI/JER/IOM/ABZ/INV? Because it wasn't cost effective to have 2 aircraft or less, it costs a fortune. I'm not going to spout the figures on here for obvious reasons.
How many bases do Ryanair operate from where they have only 2 or less aircraft in base? Probably not many.