In addition to the JDK Domino/Notes bring a lot of Jars that linger around in .../ext and some other directories. All of these should be separated and hidden from Java code in databases. They cause disturbances and we could not rely on them because we can't be sure they'll be there (in the same version) in future Notes/Domino releases.
One example is the inclusion of POI that made apps incorporating an (other version of) POI dysfunctional.
Another example is the broken ICU4J in Domino 11.
Just keep this stuff in a separate folder that is not in the classpath of the JVM. From there it could be accessed via an additional ClassLoader (which is a sibling of the ClassLoader loading user code) without causing disturbances.