- 5 million / 148 million is 3% down from peak for Russia.
- 2.5 million / 128 million is 2% down from peak for Japan.
Most importantly, Russia's population decline (which started before Japan's) has leveled off. It hit a local minima in 2008. It has wobbled up and down, but stayed close to 143m for almost 20 years [1].
This is how populations usually work; they level off and oscillate around their carrying capacity. It's often studied in biology [2].
Shaving off 3% of the population of a country doesn't lead to deserted cities any more than other factors do. Natural resource depletion and economic factors are and will most definitely keep being bigger worries for cities (ie, droughts leading to water shortages, big employers moving out, etc).
[1]: https://data.worldbank.org/indicator/SP.POP.TOTL?locations=R...
[2]: https://www.khanacademy.org/science/hs-biology/x4c6733622308...