Using the JSO methods in a setup similar to http://biomodel.uah.es/Jmol/JSO/simpleJmol4.htm, with unsigned applet, no jQuery , no ChemDoodle etc. options active.
(Jmol 13.0.RC5, Firefox 13 Win)
I see the applet normally. If I disable Java, instead of the warning in yellow square, a blank square is displayed.
It seems that the browser is getting a non-specified image substitute. This is the relevant generated source:
<div id="myJmol_appletdiv" style="width:100%;height:100%">
<img id="myJmol_image" src="" height="300" width="300">
If the (server-side?) image generation is not available for whatever reason, the old "please install or enable Java" note should be displayed --it is indeed implemented in JmolApplet.js