It is true, of course, that low interest rates have many effects. Some of these are intentional – they make it cheaper to borrow money, spur investment, revive growth and, eventually, stimulate inflation. But they also have unintended side effects. So yes, for savers low interest rates do mean that their money accumulates at a much slower pace than before.
When central bank money, which provides the unit of account, is converted without friction to and from other forms of money, this makes it possible to ensure the uniformity of money; in other words, maintaining a situation where "one yen is one yen," regardless of payment instrument.