Opting for an Intellijel Shapeshifter but discovered two kinds of faceplates. Now I’m wondering if it’s only the faceplate that’s different or perhaps also the firmware. I see ones where there is only Shapeshifter mentioned on top (and one red marked output), others have Cyclonix Shapeshifter on top (with all black marked outputs).

Faceplate with Cyclonix is the oldest version.
It runs the same firmware.

I read somewhere that the wave folder behaves differently (it doesn't cut out the audio completely, when fully CCW), on the newer model, or something like that. Anyone care to clarify this?

I messaged Intellijel about it:

Yes the module itself is the same. There were a few revisions of the module that will be displayed on the rear PCB, but the differences are quite minor. For example, the first run would close the VCA at the FOLD output if the FOLD knob was all the way down.

They can all be updated to the latest firmware of 2.04.