Japan is Japan, why they do not call it the Japan or the Japans?
The US is a short form of United States, because there are many states and as one entity, it is called States.
The same reason is applied to the Philippines.
There are many islands in the territory of the Philippines and as one body, it is the Philippines.

But nobody says the Japan, nor the Japans, even though there are many islands in Japan.
If the same rule is applied, we would call it the Japan or the Japans.
It is clear that there are many irregularities and ambiguities in languages. Languages themselves reflect the inconsistencies and discrepancies of users, that is us. So, good language learners are those who accept and enjoy those traits of languages.