It’s not the cable, I’ve tried others (as well as going straight to amps instead of through my pedalboard) and these are Mogami as well.
There is probably some amount of EMI from my computer and studio monitors that are close by and that’s just kind of unavoidable, but it isn’t a problem with the other guitars as it is very low level noise and using a noise gate deals with it without really changing tone at all. Only with some guitars and pedal combinations (like the Explorer w/a Nailbomb in the bridge going into the Dirty Tree) does that noise ever require a tweak to the noise gate.
The thing with the EMG’s is I’m using the solderless electronics. Wired up as normal the noise doesn’t change when touching anything except the ouput wires that run from the volume pot to the jack, or the circuit board of that pot, or the retention clip of the jack that connects to the cables ground. Touching the metal knob shaft of the pot doesn’t do anything for instance. That to me seems like the ground is connected as it should be, it just is open to being interfered with between the volume pot to the jack because there’s nothing shielding those wires or bare metal parts of the path.