MrV: cloning is a good thing, no need to load the model twice. the only issue was in trying to apply an effect when it isn't needed, the clone already has the effect cloned over from the original.
animated objects can be both cloned and instanced without issue, however instancing is more limited and tightly bound to the original. you can basically position and rotate independently and that's about it. anything that needs to animate or modify limbs independently from the original must be cloned not instanced.
characters generally need to be cloned
a single animated tree can be instanced
a clump of animated trees as limbs within an object that position the limbs to fit the terrain must be cloned
a single static rock can be instanced
a clump of static rocks add limbs within an object that position the limbs to fit the terrain must be cloned
and so on