This is a situation where a little bit of forthrightness would go a long way. It’s worth pointing out that Popova, by not disclosing this anywhere on her site, is likely violating FTC rules. She could easily fix this, be straight-up about it, and go on her way. But if these allegations are accurate (and yes, a casual observation shows she’s using affiliate links), it exposes her for being hypocritical and could foster a backlash.
Really, this all could have been solved with a short little blurb on a page somewhere. Which is to say: Always. Be. Transparent.