Thanks - I will keep the symlink in place and I won't touch the Deploy bundle, because I need the plugin in Safari and I don't need Oracle's Java 7 for now...
If the plugin is supposed to stay in the Deploy bundle, this could help others who miss the plugin - they could just recreate the symlink, right?
To summarize I think we can state, that the Java update 2012-006 for Lion and Mountain Lion sometimes leaves the symlink in /Library/Internet Plugins/ untouched.
The circumstances that lead to this behaviour are still unknown.
The install log in Console shows that the scripts to create links and to delete obsolete files ran okay, but there was an error with the "postinstall" script. In spite of this the installation succeeded:
Oct 20 16:24:52 michaels-imac Installer[284]: Java für OS X 2012-006 Installation Log
...
Oct 20 16:25:56 michaels-imac _securityagent[305]: Running Install Scripts . . .
Oct 20 16:25:56 michaels-imac _securityagent[307]: Begin script: createlinks
Oct 20 16:25:56 michaels-imac _securityagent[309]: End script: createlinks
Oct 20 16:25:56 michaels-imac _securityagent[310]: Begin script: deleteObsoleteFiles
Oct 20 16:25:56 michaels-imac _securityagent[314]: End script: deleteObsoleteFiles
...
Oct 20 16:25:56 michaels-imac _securityagent[318]: Running Install Scripts . . .
Oct 20 16:25:56 michaels-imac _securityagent[320]: Begin script: postinstall.sh
Oct 20 16:25:56 michaels-imac installd[295]: postinstall: launchctl: Error unloading: com.apple.mrt.uiagent
Oct 20 16:25:56 michaels-imac installd[295]: postinstall: com.apple.mrt.uiagent: Invalid argument
Oct 20 16:25:56 michaels-imac installd[295]: postinstall: launchctl: Error unloading: com.apple.mrt.uiagent
Oct 20 16:25:56 michaels-imac installd[295]: postinstall: launchctl: Error unloading: com.apple.mrt
Oct 20 16:25:56 michaels-imac _securityagent[334]: End script: postinstall.sh
...
Oct 20 16:25:56 michaels-imac installd[295]: Installed "Java für OS X 2012-006" ()
...
Oct 20 16:25:56 michaels-imac Installer[284]: Displaying 'Install Succeeded' UI.
Does anybody know what "com.apple.mrt.uiagent" and "com.apple.mrt" stands for?
Obviously the "postinstall" script provides an invalid argument (at least on my system).
I have no idea if this is related to the Java Plugin symlink not being removed...