Hardly *any* websites still have java applets. *as a java developer* I haven't even seen one for i don't know how long. Java does indeed still have its place(s) but applets are deader than a dead thing.
Flash is thankfully getting rarer too. My feeling now is that any site that only offers video as flash, or like BBC insists on serving flash to desktop users despite it working perfectly well using HTML5 if you force it, just don't really want me to watch their videos.
That's why you leave Javascript turned On in Safari. What you want to remove is Oracle's JAVA.
Some users may search for anything that says Java, and remove what shouldn't be removed.
I also installed AdBlock in Safari, and that made it even better.