Looking back at my booking sheet, about 1 in 5 or 6 was a 1-night stay. Probably because my home is only a 20 minute trip (off peak) from the airport.
Then, about 4 months ago I was asking myself the same question you are. The decision was made for me when I had five 1-nighters in a row in one of my rooms and another two 1-nighters in the other room at the same time - right at the point where I started working random casual shifts. And that was chaos!
Basically, the choice came down to:
1/ cancel a booking or two - NOPE!
2/ work myself to frazzle
3/ block off a day in between arrivals and know I was going to have no income for that night
4/ set a 2-night minimum stay and see what happens.
I went with Option 4 and haven't noticed a drop in bookings or income. I still run both rooms to at least 90% occupancy (except for Christmas).
All the best with whatever choice you make.