The yFiles license terms state that the yFiles classes need to be obfuscated before they are delivered as part of your own application to a third party.
yWorks provides the cost free obfuscator yGuard which fulfills the minimum requirements as outlined in the license terms.

Please see the Obfuscation appendix in the yFiles for Java Developer's Guide for more information regarding obfuscation benefits in general, and the obfuscation process of a yFiles-based application using yGuard specifically.