The absolute value of the base unit of the currency doesn't matter. The Yen is not more devalued than the Yuan simply because it's base divisible unit is smaller. In fact, most would say the Yen is severely overvalued, and it's putting strain on the Japanese economy. This is one reason that Shinzo Abe is giving the Japanese central bank leeway to print more money, to lower the value of the Yen and make them more competitive again.
How "overvalued" or "undervalued" a currency is depends on market factors. China plays games like buying US debt to make the dollar stronger to make the Yuan weaker in comparison - this is what people speak of when talking about these things. Not the absolute value of the divisible unit. The Yen could easily just declare the base unit to be some denomination that is worth a hundred yens, they would become a hundred times more "valuable" by your metric, but it would have no real effect.