I've not played with the MEKANISM mod but from what I read on the Wiki there is no upgrade as it is the highest level multi tool available in the pack. So as long as you keep it charged up with RF and remember it does not block attacks you have the best tool already.

Can atomic disassembler be enchanted?

Either through legit methods or by using cheat commands? Figured out that enabling Creative Mode and using an Enchanted Book and the tool on the anvil will work.

How much damage does an atomic disassembler do?

Sword - Although a very formidable weapon dealing an average of 10 hearts damage (20Hp), the Atomic Disassembler cannot block attacks.