When you enchant a nanosaber the enchantments treat it as a tool and not a weapon so it gets enchants like eficiency and silk touch.
Already known, the devs are working on adding an "IsEnchantable" hook to Forge that will prevent IC2 tools, weapons and armour from being enchanted.
Unless, this is already in Forge, then I recommend updating. Not sure if previously enchanted IC2 things will crash or bug the game, so back the save up, just in case.
You are not supposed to enchant any IC2 items.
Ennchanting IC2 stuff will be disabled for ALL of the items related to IC2 in a future release.
Stop using enchantments (pretty much period) and you should be fine both code wise and mentally.
I am totally and utterly Christmas eve drunk, anything i post today might be full of spelling errors and typos and ramblings and other hilarity.