I noticed that two of 3 of my non-profit poetry sites have dropped out of the Yahoo directory (one for kids and one for adults)--they have been there for several years.
And there is no form to submit non-profits anymore either.
One of three links to your "non profit" content remains. On that evidence, it seems indisputable that Yahoo is not dropping non profits at all. Just link to your other content from your listed URL, and you'll be in as good a shape as if you kept all your personal content on one domain.