I don’t recall the department of Justice questioning the national injunctions legality at that time though, tbf.

That's all this ruling is about, whether a circuit court can issue a national injunction. I'm assuming that this specific question hasn't been asked to the SCOTUS before (because it's a stupid question that shouldn't have even been entertained). The EO is still enjoined in the jurisdiction of the circuit courts where a challenge to the EO has produced an injunction. So the EO itself is still going through the courts.