The belt transport is the most CPU-intensive part of this mod, even with the optimizations I've done, and changing it to preserve item health would add a very significant amount of overhead. I suppose I could add a config option to preserve item health, however that would make Factorissimo significantly less performant (since every single teleported item needs to be transported as a full LuaItemStack instead of a simple stack). Of course miniaturization would reduce the amount of teleported items, however that would only help when it is done consistently.
PPE: In fact, I checked the API and right now it isn't even possible to read the health of items on belts! I'd have to ask the devs if they could add a new API method.