Right, it’s a bit of a damned if you do, damned if you don’t situation for Apple. Being more proactive at removing or blocking clone apps makes it more likely that they’d run into some of the same abuse YouTube’s ContentID (and human reviewed copyright claim) system experiences (false claims of ownership, uploads of songs using permissively licensed samples*, use of copyright measures to silence criticism, lack of protections for fair use), on top of inevitable developer complaints that would result in increased regulatory demand. With a more laissez-faire by default approach, they open themselves up to lawsuits like this one.
* Think songs that sample the so-called YouTube Audio Library, then get uploaded to ContentID, where the uploader goes on retroactively to claim monetization on all users of the original track.