I have just installed 2.1 which seems to include CDK, but I do not see any relavent nodes.
You have to install the CDK Extensions first.
Start KNIME 2.1 select Help>Software Updates…
Click the tab Available Software and expand KNIME & Extensions Update Site.
Under KNIME & Extensions you can find the “KNIME Base Chemistry Types & Nodes” and “KNIME CDK Chemistry Feature”.
After confirmation of the license and restart of KNIME the Chemistry nodes should be available in the node repository.