Yes, DIN 41612 in its 3x32 format is one of the densest 0.1" pitch connector systems that are readily available. If the devices already have leadout wires attached, you can get DIN 41612 female crimp shells and contacts, which although a PITA requiring specialist tooling (i.e. a ratchet crimper with the correct die for the contacts and wire size, an insertion tool and a removal tool for your inevitable mistakes) is preferable to having to do wire to wire splices.
Also for either ordinary 2 row IDC or DIN 41612, consider getting right-angle male connectors and mounting them at the board edge. It resolves the vertical clearance issue and provided you leave 'finger space' behind the ends of each connector, lets you use a two handed pinch grip to provide the insertion force, without bending the PCB. Another refinement for IDC connectors would be to mate them with latching box headers on the PCB not ordinary pin headers, as cams on the latch arms partially eject the cable connector when you fully open the latches, reducing the risk of damage when disconnecting.