First, Johnson v. Eisentrager, was narrower than that, only holding that US courts lacked jurisdiction to hear challenges from enemy military prisoners who at no point had been held in the US.
Second, it and the broader idea that those detained by the US government have no rights cognizable under US law or enforceable in US courts were subsequently contradicted by Hamdi v. Rumsfeld (US citizens detained in conflict, even entirely overseas, retain Constitutional due process rights), Rasul v. Bush (military detainees have right to habeas corpus review of detention in federal court; this and subsequent cases in this list all deal with non-citizen detainees), Hamdan v. Rumsfeld (in a habeas challenge as allowed under Rasul v. Bush, finding the military commissions instituted at that time at Guatanamo illegal under both the Geneva Conventions and the UCMJ), and Boumedienne v. Bush (section of the Military Commissions Act of 2006 purporting to strip detainees of habeas corpus rights was unconstitutional and detainees retained those rights.)
Practically all of these have a gaping martial exemption.
That said, as far as I know, martial law has only been declared at the federal level once, in 1863 during the Civil War, so I’m not sure what that has the do with anything.
Then there’s the US who has consistently held that those rules only apply on US soil (hence Guantanamo) and that the rules only really apply when it comes to US citizens (lawful permanent residents get a slightly more diminished “store brand” version of the protections).