I'd actually thought a decent bit about this; it should be possible to track your buff gain messages and when you see a buff that pertains to a given trinket, start the "hidden cooldown" timer for that trinket; on the character screen you could have a cooldown graphic and everything.
Something less advanced, but no less functional, is to download my mod
SpellWatch (soon to be hosted in the wowace svn!) and set up a timer for a self-buff with the right name and duration.