Yes, that is how Glyphs deals with new axes internally. It will create a unique id first. When you reopen the file that id will be resolved to something more reasonable by still being unique along the other axes.
I guess you should not use the long identifier, as they are basically throway-ids.
For example, I want to build a custom designspasce relying on additional axes properties. Consequently, I need to extend the behaviour of the axis class.
Being able to reference an axis by its ID would enable me to add new functionality to the axis object without modifying its code.