You're right, but not 100%. Cash flow alone isn't enough to prove damages. You have to prove both that the devs are making money off of it AND that Nintendo is losing money because of it. Generally courts will assume that 1 pirated game = 1 game gone unpurchased (which is ridiculous) but they'd still need to prove that Atmosphère is endorsing piracy. So being vocally against it, or what you call "all the moral stuff people come up with", is actually judicially relevant, though less so than cash flow.At the end of the day Nintendo doesn't want any unlicensed software running on their locked console and that would include Atmosphere as a replacement firmware. As said before the only saving grace is that it's not paid software, all the moral stuff people come up with is irrelevant from any legal point of view.
Easy way to keep Nintendo away? Stay non-profit. It takes cash flow to prove damages. If there was a Patreon for Atmosphere Nintendo would be all over it, so far SciresM has played it smart by not even taking donations.