Hi Hugues,
I just installed the 3D-e-Chem extension without a problem and it has the Silicos-it nodes in it. This is the update site I used and I am running MacOS. http://update.knime.com/community-contributions/trusted/4.1
Could you please check that you have the right update site in your list of update sites? You can also try a fresh installation of KNIME to see if there is some dependency problem/conflicts in your current installation.
Let me know if this helps.
Best,
Temesgen