I think it depends on what you mean by "dark matter" and "dark energy". If you think they're theorized substances or energy sources (which seems to be the preferred interpretation in the press), then, yeah, there seems to be a decent chance that that will be the case.

If you think, as more cautiously-minded folks seem to, that they're just clever catchwords to describe troubling lacunae in our understanding of how the universe works, not so much. There really are observations that we have trouble explaining.

If black holes don’t exist, what happens when gravity overpowers electromagnetism and the strong force in a region of high mass concentration? I don’t get what the alternative hypothesis could be. Do we just get arbitrarily-large neutron stars or something?

Something like a fuzzball:

https://en.wikipedia.org/wiki/Fuzzball_(string_theory)

But there I think most physicists think something like the solution to the Einstein field equations does obtain within most of the interior region of the objects we call black holes. They just believe that the region of the singularity may have some other physics so that it doesn't become singular.

What does dark matter have to do with black holes?

They are related topically in that yesterday new research cast the very existence of dark matter into doubt, and this blog post is kind of trying to do the same (albeit with less rigour than the actual scientific paper posted here yesterday).

As another reply mentioned, the paper in question cast doubt on one of the key pieces of evidence for Dark Energy, not Dark Matter. Despite the similar names, they are not fundamentally related concepts and there is significantly more evidence for the existence of Dark Matter.

Wasn't that dark energy in yesterday's article?

Dark matter is NOT the same thing as dark energy.

Well, MACHOs are one hypothesis for explaining dark matter, and they're typically considered to include (but not be limited to) black holes.