Yes, there are Muslims in Japan. Not many, but there are. And yes, it's ok to be friends with them.
The prophet Muhammad instructed his followers not to make friends with the non believer. It's in no one's interest to be friends with people supporting such an evil ideology. Unless you're an idiot.
You've never had a conversation with a Muslim person for longer than 5 minutes, have you?
I worked with several people from Egypt and Lebanon, who were Muslims. They were Muslims to about the same degree as lots of Christians - including myself - are about Christianity.
The word AGNOSTIC comes to mind, followed by "I don't care who you are as long as you leave me alone".
We were friends. We hosted each other in our homes.
Those Muslim friends never indicated to us that they ever wanted to be anything but good Canadians.
Muslims of yesterday were decent people. Muslims of today.... Not so much.