If the flora is placed as a flora object in editor, or generated in random scenes, it will be handled as flora, where as the engine will use static batching on them and what not, so don't instance them yourself.
Note that you _always_ should have a LOD4 stage for all your flora (plants/trees etc anything that is placed as a flora object in-editor) and note that how the engine batches things, you should have a LOD4 stage that is not more then 300 verticles, preferably a lot less.
About instancing weapons, that could work out just fine in most cases, but, except the motion-blur-disappear issue.. There is another nasty side-effect with instancing; Basically the engine renders the vertices less accurate on a position in the scene, which could mean that when your 10 meters away from your weapon, and the weapon has multiple faces on top of each other (think of having a ring on top of the wood of a musket) the engine sometimes renders one verticle on top of the other and the other way around and you will see a constant flickering of these faces over each other which is problematic.
Scene props, generally don't have multiple faces on top of eachother, where as weapons usually do. But you could look into what to instance or not on a case by case basis.
Note that Instancing reduces CPU usage, but only in the DirectX thread, meaning if you have a multi-core machine, you will not notice any difirence, but users with bad CPU's will notice the change.