I didn't notice the glossary and I am actually glad I didn't. By the end of Anathem all of the strange names for things become second nature and you understand from the context what their meaning is. It is almost like what happens when you learn a new language and are able to think in that language.
Also, if you enjoyed the Shaftoes and Waterhouses of Cryptonomicon, consider putting the Baroque Cycle before Seveneves.