Most chargers (especially Li-Ion) have to detect when the battery is done charging so it doesn't explode, so they will usually "trickle charge" or shut off the charging all together. I don't know why this would be any different.
the instructions recommend that you disconnect the controller once it's fully charged.
But there is an indicator that says when it's fully charged, so it should know and not do any damage. I think the warning is just there to prevent them from getting sued in case something does go wrong with the controllers
I have never had any problems with leaving the controllers plugged into the charger. I should also mention that I have my charger and PS3 plugged into a continuous UPS which cleans the power going to the devices.