Deconstruction is the downgrading of a building. Deconstruction happens one level at a time.
Resources must be spent to remove a building, and the deconstruction takes a certain amount of time to complete. Not only do you not get any points for the resources spent on deconstructing, you also lose points from your score for all the points that that structure was worth.
Since the process is entirely wasteful, the only occasion that you would want to deconstruct a building is to free up fields on a colony, or if one of your planets is being attacked and you do not have any other means of saving the resources- the resources put in can always be recovered by cancelling the deconstruction. It is not necessary to deconstruct individual buildings if the complete destruction of a planet is your goal. To do so would only waste resources and time.
Both Interplanetary Missiles and Anti-ballistic Missiles can be deconstructed in the same fashion as buildings by clicking on the Missile Silo from the buildings section. Unlike buildings, deconstructing Interplanetary Missiles and Anti-ballistic Missiles is instant and costs no resources. As of update 4.0 the deconstruction of interplanetry missiles and anti-ballistic missiles can give you up to 75% of the resources required to make them by using a scrap merchant.