I think the most important thing is that you do well by the standards of your own institution and that you get good letters of recommendation from professors there.
Note that standards for a masters degree vary around the world. In some places very little research is required and the degree is based mostly on coursework. The "thesis" might be little more than an intelligent summary of some subfield. Perhaps something like a literature review for a doctoral dissertation. Other places the requirements are more research directed. While published papers are required in some places, it isn't universal.
But, it is in the nature of mathematics that if a research program is strictly time limited then what can be expected is also, necessarily, limited. Some problems remain unsolved after 100 years. Insight can't be scheduled.
Then, the question is, how will an admissions committee in a given place, say Europe, evaluate candidates from such a wide variety of programs and backgrounds.
Normally, it isn't a question of counting papers. Normally, it isn't any single thing. The admissions committee will be looking at what they hope is a complete record that indicates both the necessary background and a high likelihood of success in a PhD program at their university. Lots of things contribute to that. If you have done a dissertation, it will be a plus. If you haven't, but have done other "interesting" and relevant things, then those things will be a plus.
In the US this would be much less of a problem, of course. But, flexibility is required everywhere or a university would be forced to exclude too many good candidates based on things that matter less than qualities such as demonstrated focus, hard work, preparation, and potential.
Do good work by the standards of your own university, even if it isn't yet in the narrowly focused field you want to study for the PhD. Develop some insight, generally, into mathematics and especially number theory. Get good letters of recommendation.
