Most of the damage the CE does listed as being Physical, as opposed to Kinetic damage, which there is no listed resistance against. Its particularly bad from when the shards ram you (and in the chaos and backset against the CE I can't tell them apart from debris till its too late anyways). Does Kinetic armor protect against Physical, or is there something else that can be stacked for a permanent resistance, or is this meant to be untankable damage, or it is a bug?
Kinetic resistance does not protect against physical damage, no. It is likely that powers which provide "all damage resistance" like Polarize Hull protect against it, but I haven't tested that to confirm it and your space physical resistance isn't shown.
The CE's shards and the Kar'fi NPC's Tortured Souls are the only space enemies who deal physical damage.