“Domino applications that are created from system templates that make use of Java applets, such as the Domino Directory (names.nsf), Document Library, Domino Web Server Configuration database and Widget Catalog database, will be impacted by the removal of NPAPI functionality. The Teamroom and Discussion databases created from older (pre-8.5.3) templates will be impacted as well.
Additionally, custom Notes applications that are using Java applets also may not work correctly in web browsers due to these changes.
It is recommended that you either (1) redesign the portions of the applications that use Java applets to use HTML, or (2) redesign the entire application to leverage XPages design elements.”
I think IBM will not replace any Java applet.