They might decide not to counter-notice, because there's a big trap in the DMCA counter-notice: as far as I know, for a DMCA counter-notice to be valid, the one doing the counter-notice must agree to be bound to the jurisdiction of an USA court. If the youtube-dl author is not from the USA (I think he's from the EU), that would expose him to legal risk.
(As a non-USA person, to me this is the most evil part of the DMCA take-down system: even a defective DMCA notice leads to a dilemma, either you keep the content offline, or you risk being sued in a foreign jurisdiction you have no control over. This is also why I believe one should always prefer to host in one's own country, so that any dispute can be resolved by the local courts.)