How is a MSc thesis evaluated in an application to a PhD program?
Given the fact that is extremely rare to have a decent publication out of a Master thesis in pure maths, the content and quality of your thesis will be reflected on the recommendation letters.

This, together with your grades and other activities you may have would be the ticket to your admission. 

Note that nobody will read your thesis. For the admission committee should be enough if it is apparent from the letters that you did a decent work in your thesis. Your application should show that you have potential of doing research but nobody has the time (or the will) to go through a thesis document.