The only problem with that theory is that the hardware sales that Earthbound Zero created were minuscule. It is not a system seller for 99.9% of their potential customer base.
It's not even the first 1st party NES title to be exclusive to the 3DS or the Wii U and they undoubtedly gave up much more in 3DS Virtual Console sales than they gained on the Wii U side by keeping it exclusive. So I'd argue that it's simply a demonstration of their lack of interest in the 3DS Virtual Console and is symptomatic of a lack of effort across their range of Virtual Console platforms.
I have a suspicion that their NES emulator on the 3DS had issues with it and rather than simply rectify the problem, Nintendo just sat on it thinking that the potential sales didn't justify the effort.