This phrase is no doubt completely meaningless to you unless you watch an inordinate amount of Japanese anime, as I do. Let me explain. Miko are shrine maidens who perform various functions in a Shinto shrine. They may perform ceremonial dances, tell fortunes or even sell souvenirs. It is not necessarily a full time occupation and it may be filled by a university student working her way through school. It has little of the sort of religious commitment we would associate with nuns. When anime writers and producers need to portray a Catholic nun, they will dress her in some semblance of a religious habit and she may wear a cross but there the similarity ends. In the absence of any cultural context there is nothing for them to draw upon to flesh out the character. Naturally they draw upon the only thing they are familiar with. Hence in anime, all nuns are miko. This is not meant in a disparaging way... it is simply the way things are.
Christianity arrived in Japan in the 16th century with Jesuit and Franciscan missionaries, the most famous of whom was St. Francis Xavier. By the 1630's Christianity was outlawed in Japan but the churches planted by these early missionaries went underground. These became the Kakure Krisitan or hidden Christians. These Japanese Catholics continued to practice their faith in secret, meeting in homes and secret rooms. When religious freedom was restored in the mid 19th century, some 30,000 of these secret Christians came out of hiding and rejoined the Catholic Church.
Between 1603 and 1639 many of these Japanese Catholics were martyred. In 2008 Pope Benedict beatified 188 of these martyrs. During WW2, a group of Jesuits survived the bombing of Hiroshima and a group of Franciscans survived the bombing of Nagasaki.
Today the Catholic Church has about 500,000 members in Japan.