DeNA has seen drastic decline in profit over the past couple of years.
Their only money making venture, mobage, is desperately looking for ways increase revenue. What better way to do this than to offer their content on another platform?
By the same token, there's very little reason for Nintendo to buy a company that is bleeding money, but they would like a way to connect their products to mobile game audience.
Offering mobage games featuring Nintendo IP's on Nintendo platforms is a good compromise that would provide value to both parties.