The primary motivation is energy independence: currently, Japan is the world's largest importer of both coal and natural gas.
As H2 would be supplied by reformation of methane hydrates, it is still a fossil fuel and does not solve carbon emissions. But the idea is that emissions would be substantially reduced compared to the current situation, where a large portion of Japan's energy is supplied by burning imported coal and oil.
Unlike many European countries, Japan is surrounded by deep waters, which makes constructing offshore turbines more difficult and expensive. But the recent development of floating wind turbines which can operate in much deeper waters means that may change.
However, there is an argument that hydrogen electrolysis is not an efficient use of electricity. By the time you've electrolysed water, transported the H2, and converted it back to electricity in a fuel cell, you've lost at least 70% of the original energy.
So unless there is a lot of surplus electricity generation that would otherwise be wasted, it makes more sense to use it directly where possible. Storage technologies (such as chemical batteries, heat batteries) may be more economic than H2 electrolysis/distribution.
I don't know that this is helpful at all since it either burns or degrades to CO2, and is a significantly worse greenhouse gas before then.
Then there's also the eco system aspect. The environments surrounding the reserves have unique organisms. What's going to happen with that? Just because we don't see it, it doesn't seem to matter..
However, global anthropogenic emission of methane is about 300 Tera-grams per year [1]. Anthropogenic emission of CO2 is about 35 Giga-tonnes per year.
300 Tera-grams is 0.3 Giga-tonnes
300 Tera-grams of CH4 degrades in about 10 years into about 0.5 Gigatonnes of CO2. About 1.5%, one sixtieth of the CO2 problem which can last hundreds of years. Methane emissions present 10-15% of the immediate and near term problem - thats less than half, less than a quarter... seriously, its about an eighth. After 10-15 years the elimination of methane, eliminates about a sixtieth of the global warming emissions problem. This will be why the IPCC presents CO2 as the major issue, because they do find and show that it is.
[1] (Table 1) http://rsta.royalsocietypublishing.org/content/roypta/369/19...
There are many sources in broad agreeance for these heavily researched measurements. I included one recent source for methane emissions by weight, since its a bit harder to dig that up.