If a unit has already 3 damage marked and I play Imperial Decree afterwards does the unit die?

No, the unit will not die.

Imperial Decree creates a triggered ability that kills a unit when it takes damage — it does not check the state of being already damaged. The trigger condition is the event of receiving damage, not the condition of having damage marked. Since the 3 damage was already dealt before Imperial Decree resolved, that damage event has already passed and cannot satisfy the trigger.

If that same unit later takes additional damage while Imperial Decree's effect is active, then it would be killed (the trigger would fire for that new damage event).