Duet3 + SBC connections
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I had a look into the Duet3 schematics and verified that this board only uses 6 connections (5V are to be provided to the SBC from separate supply) taken from the 2x13 flat cable. If I would use just a small 6-wire cable with proper shielding, is it OK the replace that larger flat cable and free all unused GPIO pins? And what is the max length for this SPI connection?
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I'm not sure about the max length, but replacing the cable with something else is possible. With good quality conductors and shielding the length should be pretty decent. How far are you wanting to go?
You may find some useful information here: https://github.com/Duet3D/DuetSoftwareFramework/wiki/SBC-Setup-Guide