Unfortunately, most non-profits are notorious for money-laundering and illegal activity. I believe you should consider waving fees on a case-by-case basis, if you can spend money to evaluate, but if you can't, I'd err on the side of caution and not waive fees.
I understand that this is an unpopular thing to say, but I say it From research I did on building a "transparent accounting" software for non profits. I found out during the course that most of them didn't want to be transparent.
If you don't believe me, check transparency international's research on the same.
I've never heard about this, and it's interesting. Have you seen any evidence beyond your interactions with non-profits, such as a study? Ideally indicating how widespread this practice is, the degree, or the motivations / why it happens.
