It may be a similar case to the words "Uinta" and "Uintah"(one being a mountain range, the other a town on the Transcontinental Railroad), or the 19th-century spelling of "Uta", "Utah", "Yuta", "Ute", "Yutay", etc. in reference to the Ute tribe, that were all interchangeable depending on the writer. Also, in the mid- to late-19th century, the enye (the spanish character of the n with the tilde on top) was very common, especially with the word Canyon (canon).
Also, it is important to remember that when translating native american names, the writer often wrote the words phonetically as best as he or she could understand it. Thus, one translator may have spelled it Shawano, and another Shavano, but both intended to write the same word from the same language. I imagine this is the source of the difference in your case.