Is it possible to fix these "cracks" that appear when rendering in "Cycles"?
Everything looks correct in EEVEE.
Maybe the problem is how I modified the "crystal".
Blender Stack Exchange is a question and answer site for people who use Blender to create 3D graphics, animations, or games. It only takes a minute to sign up.Sign up to join this community
If you Apply geometry nodes, you can see hexagons are not flat. They are triangulated. Eevee seems to use different normal info (I'm not so techy, so I'm not sure it is calculated). Hexagons are not flat because of your Transform Geometry node, that scales vertices on Y axis. This kind of math just can't result with real flat faces. I wanted to move Dual Mesh after transformation nodes, but result was similar.
You can use just a Set Shade Smooth node and do selection for smoothing by Face is Planar node to specify co-planar faces, adjust Threshold value ...
... or you can limit Split Edges node to specify Edge Angle (I haven't used this node before so I can be wrong, but it solved the issue).