Hi J.! I'm a mother of 4 children, ages 11, 9 1/2, 6 1/2 and 3. I've always been pretty flexible when it came to them taking naps. From my experience, some children cut naps out of their day all on their own simply because they're not tired enough to take a nap. And some children need more sleep. Your sons are still young and if it works better for them and for you, I don't think it would "hurt" them to take their two naps. If they get through the day and are happier, then I would think the two naps are beneficial.
Although I've always tried to do what my pediatrician tells me to as far as the childrens development and physical needs are concerned, if my children are (or were, since mine are older) benefiting from taking a nap (or two) during the day, I prefer it. When our children are cranky or unhappy, it's hard to be a more productive parent and it can make us sad because they're not happy.
Sounds to me like you're doing a great job and as long as your boys are healthy otherwise, a couple of naps each day to avoid the "crankies" doesn't sound like it would hurt at all. You never know, as they get older, they may phase out one of those naps all on their own. :-)
Hope this helped!
A.