In the end, none of it makes any difference to consumers whatsoever.
Sony have rolled out a new batch of models for the PS4 on their Japan store. While the 500 GB Glacier White SKU of the console is still being sold under the same designation of model number CUH-2100, new variants of the console have been listed on the site with the newer model name CUH-2200.
These are the 1TB Jet Black SKU, the 500 GB Jet Black SKU, and the 1TB Glacier White SKU. All specifications of the system, however, remain completely unchanged, including things like physical dimensions, weight, and power consumption. The prices are also the same as the CUH-2100 model, at 34,980 yen + taxes and 29,980 yen + taxes for the 1TB and 500 GB models respectively.
So why the change? Well, usually this kind of change indicates that the system now just comes with new inner parts and components that replaced ones used in the older model, most likely to decrease manufacturing costs. Usually, a big, noticeable change or redesign comes with a change in the first digit of the model number (the slimmer PS4 went from CUH-1XXX to CUH-2XXX).
In this case, of course, only the second digit has been altered. The last two digits are usually changed to denote the region the system is being sold in, so we might see that change reflected if and when Sony decide to start selling the CUH-2200 models outside of Japan.