Japan was not a small nation back then, it was a well-organised country with lot of people. When the first Westerner arrived in 1450 there was around 10 million people in the country, England as comparison as 2 million at the time.
Wen Japan closes it off from the outside wold in 1650 there is around 25 million people there compared to 5 million in England
Japan is not a small nation, it would be hard and expensive to take control by force. If you look at China they alos hold off the western nations. It is the Opium wars where that first started in 1839 That was the first large war between China and a western power
Japan open up after the Perry Expedition in 1853. IT is in the 19th century the western powers advanced their military enough to have a good chance of waging war against Japan and China. Even if you have a technological advantage you need enough troops to win and transporting enough will be had and expensive so a war before that is quite impractical.
Japan then start to westernize and develop its military quite quickly. In 1905 they won a war against Russia primary at sea, this is a turning point in western military supremasy. Russia really try to win the war with most of the fleet sailing there from Europe and get crushed in the Battle of Tsushima.
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