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Ok, you are running the server in your home network. I thought it would be in a DC.

I am not using IPv6 at home. My ISP did not use IPv6 for the longest time and I deactivated everything IPv6 (even on a kernel basis on my Linux VMs). Thus my home network is entirely IPv4.
I believe that the ISP now supports IPv6, but I would have to verify this and change my settings on my VPN/router which is an OPNsense box (the cable modem is in bridged mode and connected to it).
Currently I only request an IPv4 address.

I experienced from my office at the university that I cannot even connect to my nextcloud Landing page when my PC has not an IPv6 address.

Hmm, isn't there a bridge between IPv4 and IPv6, irrc it's called NAT64.

With an IPv6 address I reach the Landing page of my cloud, but not the sync target of Joplin.

With a browser you can reach one but not the other? Or do you mran Joplin cannot connect to the sync target?

Over my cell phone I can sync with Joplin using mobile data, not WiFi … therefore I think my nextcloud and my Joplin instance is configured correctly.

Yes, this makes sense somehow and I think confirms that this is a nodejs issue.
On mobile the OS stack is used for communication (which also explains why the connections are h2), while on desktop the connections are made via a nodejs module.
This module can't do h2, and apparently also has issues with IPv6.

In this case I believe we are out of luck unless the module supports IPv6.

Please open a new issue in github for tracking purposes (you can also call it Joplin sync failure on IPv6 only networks) and I will label it accordingly, so that it is not closed by the bot.

But since this is most likely an upstream issue, I am not sure what we can do. But werespective module.