I find assigning objects through scripts easier that via the inspector.
One of the advantages(e.g) when Instantiateing a prefab with a target variable that variable will allways be empty unless you pause the game and put the target into the slot manualy. If you do so through script it will find the target witch is a automated(automatic?) process.
You can also look at it like this. Do you prefere manual or automatic gears in a car? It is a preference / opinion, but I find assigning objects through script has more advantages(automatic).