Disclaimer: This answer may or may not be different in Japan, due to cultural differences. If my answer disagrees with one with experience in Japanese academia, I'd go with their answer. It may even be different between different labs and fields. But this is based on my experience and also on what I've seen since in other labs I've worked in.
I was in Australia on a summer internship and I reached out to an academic at a local university who worked in my field of interest, after reading a few of his papers and checking out his website. I informed him that I was an interested potential PhD applicant who was about to enter their final year of undergrad, and I asked him if he'd have some time available to chat with me in his lab. I attached my CV to the email and wrote a very brief paragraph with my history (a few sentences; don't give them a huge thing to read). He replied immediately, very interested, and we scheduled an appointment for some days later. We ended up talking for a few hours and he took me around the lab, and introduced me to everyone. I was 100% into doing a PhD with them -- it didn't work out for logistical reasons, but this is unrelated.
An undergrad taking the interest and initiative to read papers, check out the research, and reach out to potential PIs is considered a very good thing. It means that you are taking the PhD / Masters as the serious and professional endeavour that it is. Especially when the undertaking involves moving to a foreign country, it implies that you are considering not only whether you are a fit in the lab, but also how living in the country could impact you.
It's always considered a good idea to reach out to your potential advisers in some way, and not everyone does this -- many advisers get blind applications. If you meet them, it gives you both a chance to see if you'd be a good fit -- academically and personally. Both of these matter. If you don't get along, working with them could be a nightmare! And that goes both ways. That means that when the PI is looking at the pile of applications at their desk and designating their interest, they have something to look back on. It's definitely something that will make you stand out. Enthusiasm is great.
Of course, admission isn't decided by the PI themselves much of the time, but by an admissions committee (not sure about Japan but this is usually the case in NA and EU). Especially so when you are applying for a scholarship. But an established relationship with the PI is certainly helpful and it indicates seriousness on your part.
Finally: What's the worst thing that could happen? If you're already going to be in the country, the worst thing is that they could say no, and you still get a nice holiday. Just don't send many follow-up emails if they don't reply.
So personally, I'd encourage you to reach out to potential PIs and ask, politely, if they might have the time to briefly meet with you to discuss their research and your research interests. But definitely either ask somebody who has been in Japan, or google social norms and etiquette since that is very important everywhere, but especially in Japanese culture.