Thank you for your answer!
The installation of Webinoly on this server was in April/May 2021. But I copied some older websites over from another server. The last website I copied over was created in Nov 2020, and it still has the "include common/yoast-sitemap.conf;" in the file.
The file I changed (/etc/nginx/sites-available/example.com) does exist - even for the site I created in January 2023. Also, the yoast-sitemap.conf file exists on my server.
Anyway, the sitemaps from 2 websites I created in July 2022 and January 2023 did not work as of today. I saw it in Google Search Console and manually checked it. Maybe the sitemap from the site I created in July 2022 was working at some time - I did not check it before today. The sitemaps from my older websites all work. And after adding the line as described above, the sitemaps worked.
I do not need any custom Nginx conf, but just the sitemaps.
So, either with my "old" installation of Webinoly, sitemaps are not working without adding the line I described above, or the way I created the websites (sudo site example.com -wp=[]) breaks the sitemap support.
How can I further investigate this issue?