Adding bonds to the supercell is on the todo list: building supercell adds atoms without bonds · Issue #655 · OpenChemistry/avogadrolibs · GitHub
I’m less sure about copying partial charges. Right now the code invalidates the partial charges (among other things) when the molecule changes. That’s obviously the right thing to do in most cases. Seems like it should be okay when making a supercell, but I’d need to think a bit about potential exceptions.