To quote wikipedia:
on 5 January 2011, Adobe Systems, Google Inc., and Mozilla Foundation finalized a new browser API (dubbed NPAPI ClearSiteData). This will allow browsers implementing the API to clear Local Shared Objects.[11] Four months later, Adobe announced that Flash Player 10.3 enables Mozilla Firefox 4 and "future releases of Apple Safari and Google Chrome" to delete Local Shared Objects
So things aren't as bad as they could be, clearing cookies in firefox at least deals with LSOs if flash is up to date. Not experimented with the others, but presumably they had time to do it.
And yeah,for me java is disabled except when needed. just good sense.