Customs has always been able to search everything without a warrant or suspicion when crossing the border. I guess this is saying that they can search the digital contents of physical devices/media as well?

Not everything. From the case itself:

"To be sure, nonroutine searches, which are “more invasive searches, like strip searches, require reasonable suspicion.” Id. But we have held that “the label ‘non-routine’ should generally be reserved for intrusive border searches of the person (such as body-cavity searches or strip searches), not belongings.” United States v. Levy, 803 F.3d 120, 123 n.3 (2d Cir. 2015) (emphasis added)."

It says they can manually search them. According to this, the ruling explicitly doesn’t say if they can digitally search them.