Even if the underlying structure contains it, the RDKit 2D Depiction will be displayed as flat structure. If the renderer is changed to Marvin the stereochemistry is displayed as it was loaded originally. This is confusing and I don't understand why this is omitted in the 2D depiction?
This is a known limitation of the current RDKit molecule renderer.
We're working on it and hope to have a much improved version in a future release.
If you download the BioSolveIT nodes, then you can use the "Naomi" renderer as default in KNIME - in my opinion it is the best renderer available. This node can be used free of charge as can the node for generating good quality 3D coordinates.