Even though the national population is shrinking, the population of Tokyo is growing.
Tokyo's population is also projected to go into decline by 2020, at which point all of Japan's prefectures and major cities will be declining.
http://www.newgeography.com/content/005042-peak-people-japan
Japan ranks 27th on GDP per capita (PPP), which is pretty good. In fact it's mostly a reflection of their unusually old and retired population. If you looked at GDP per capita excluding retired people, they would likely be in the top 15, maybe top 10.
"they're struggling with deflation"
Deflation normally leads to lower consumption and unemployment. Is Japan struggling with unemployment? Nope. 3.2% in Japan, which is incredibly low.
It's interesting how foreigners tend to have a distorted view of Japan's actual economic performance indicators. You can look at a lot of them, but ultimately what matters is that people have jobs and make money, so the unemployment rate and GDP per capita is what matters,¹ and Japan is doing very well according to both.
"population is declining"
That's the only factor you correctly identified. A shrinking population means lower demand for housing, hence lower prices.
¹ Actually some economists make the point that what matters is happiness, but it's hard to objectively measure it.