100% transparent parts with shadows off could be used as collision boxes for complex imported meshes (default collision decomposer doesn’t work well)? Or is that a performance hit? Are such parts still rendered some-have?
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I use it, nothings wrong when I do it.
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Using a layer of transparent Parts as a way to get more accurate collision boxes is very common practice because it works fairly well in most situations that require it.
You should search around the forums here before making threads, as I know this has been discussed at least a few times 
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Like mentioned, it is very common. In fact this technique is even used outside of Roblox, for example many developers use simple transparent shapes for smaller items such as weapons - granted for a different purpose (mainly to simplify collisions where necessary) but none the less it is common practice within the industry. I personally do this in unreal engine aswell.
This is also used for skinned meshes. Instead of recalculating the collision per frame, multiple simple meshes are used for arms, legs, the body, etc.
Here is an example of CS:GO's character hitbox.
