I have a 3 and a 1 in my 54, and I might like a little more flow, but I can't imagine two 3's in a 40 gallon - that would be some major flow IMO, I don't think I'd want so much.
I kinda like having the two different koralias, because there isn't a lot of room from one side to the other in my corner bowfront, so this allows there to be an area of "low to medium flow."
I think you will regret going with just 1's. When you first start it up, it seems like a lot of flow, but within a week or so you'll be wishing it was more.