You're jumbling what LV actually did with the simplification of what they did.
No. The illustrations were not direct copies.
The DMCA takedown notice must meet each element as specified by law. In particular, the notice must explicitly identify the copyrighted work as well as the material claimed to be infringed.
In their DMCA notice, LV failed to meet the requirements for a valid DMCA takedown notice. By failing to specify their own work, as well as what materials in particular were allegedly infringing, they ensured that their claim was invalid on face.
As a result, LV isn't going after anyone. An invalid takedown notice carries no duty to act on the part of the service provider. It, quite simply, doesn't exist. The really remarkable thing here isn't that LV filed an invalid notice--it happens all the time, particularly when they're automated in other circumstances--but that Github acted on it at all as an invalid takedown notice is not considered by the courts to impart actual knowledge of infringement.
In effect, if it's invalid, the takedown notice doesn't exist.
And also than they haven't been running around issuing DMCA's to every _other_ flat UI style everything.
Clearly, they believe specific assets were copied to the point that a DMCA was appropriate. Pending a full post from LV, I'm giving them the benefit, as I'm certainly not giving the benefit of the doubt to the designers who so thoroughly ripped LV's style.
Should that post never come, or its contents show LV as trying to enforce a copyright on something that was merely "inspired" and not copied, I'll change my tone.
Refer to Perfect 10, Inc. v. Google if you're curious.
The DMCA ("Digitam Millenium COPYRIGHT Act") provides the take-down mechanism as a means to take down copyright infringing content, and in exchange gives the hosts of that content a safe-harbor[1].
So when people say "they don't own turquoise", those people are correct. LayerVault does not and can not hold a copyright on turquoise, or on their style of icon, and thus does not have the right to issue a copyright DMCA take-down notice for content made in the same style as their own.
[1] If a host follows the DMCA take-down process, in theory they're safe from being sued for unwittingly and unintentionally hosting copyrighted content. in practice, those suites tend to happen anyway, with the claim that the infringement was knowing -- see also youtube, megavideo).