Good question but one that has been asked before right here.

Basically, Japan was close enough to the Asian mainland that they were exposed to much of the same Eurasian diseases that Europeans would have been carrying. People in Mainland Asia and Europe were not too isolated that diseases couldn't spread across the continent, so the Japanese had little to worry about.

Related to the premise of your question, I'd suggest checking out /u/anthropology_nerd 's post Myths of Conquest, Part Seven: Death by Disease Alone which is a really good summary of why the 95% deaths from disease alone isn't an accurate story.

In that post /u/anthropology_nerd writes:

We hear that an infectious organism like smallpox, which historically has an overall fatality rate of 30%, killed 95% of infected Native Americans. Taken without reference to the greater ecological situation, and assuming the validity of colonial mortality rates (a large assumption), the myth arises of an immunologically weaker Indian population unable to respond to novel pathogens.

Circling back to Japan, even though Japan has been in continuous contact with the Asian continent for all of recorded history, you're actually on to something about the spread of disease to the Japanese archipelago, although I'm going to talk about the Edo period (1600 to the mid 1800s), not the original period of European contact. Japan's geography and history has contributed to an interesting pattern of disease spread in the case of measles: the one infectious disease whose history in Japan I've read about most thoroughly.

According to Japanese population and epidemiology historian Ann Janetta, measles did not become endemic in Edo Period Japan until the 1860s. That is, the country went decades at a time without any measles cases. Because of its geographical isolation and a population spread out along well defined travel lines, measles would come in via the port of Nagasaki, tear through the population along the main routes, infect much of Japan, and then run out of victims and disappear from the islands.

In Europe, during this same period, measles would come around to a region every few years, infecting mostly children, as adults had already had the disease. In contrast, during the worst measles epidemic of the Edo Period: the epidemic of 1862, it's estimated that up to 63 percent of the Japanese population came down with measles, spread from a foreign ship docked in Nagasaki. The victims were mainly those 26 and younger, since the last measles epidemic had hit Japan twenty-six years before. In a year that also saw a huge cholera epidemic, and an era full of disasters and fears of foreign interference, the measles epidemic was a terrifying experience with a large death toll.

However, Janetta makes the very interesting argument that massive measles epidemics every couple decades were ultimately much less deadly for the overall population than endemic measles were in Europe. The majority of deaths in a measles epidemic are of children under the age of five. In Europe, with a regular epidemic every four to five years, all children in the most vulnerable age bracket would run the risk of contracting measles. In Japan, the disease was way more likely to hit healthy young patients past the earliest years, and so, while a huge epidemic with many deaths might seem worse, overall, there was a much lower death rate from measles.

I've gone into this example of measles because I think it points out that epidemiology is complicated. In the case of measles in Japan, a big disease hitting a population largely without resistance may have worked to their advantage, because they otherwise had a healthy state of society. Meanwhile, warfare, starvation, slavery etc. in the Americas could tip disease over the edge to destroy their societies.

My main source for this post is Ann Janetta's Epidemics and mortality in Tokugawa Japan: 1600-1868 (1983).