I believe you, I’d just like to know what specifically triggers that message (simple login? viewing logs?..) so I can guess which specific service to look at and think about the implications on cgroup permissions to give you a better debug experience 
Personally I use a grafana dashboard, using victoriametrics to gather the specific stats I need. Indeed not very plug-and-play. This post might be helpful: Explaining modern server monitoring stacks for self-hosting with NixOS
There’s also icinga and nagios for more integrated solutions. Basically, any of the alternatives that focus less on doing administrative tasks (since those should only ever be done with nixos-rebuild, which nothing reasonably supports) and more on monitoring.
That said, clearly someone’s maintaining cockpit, and we should figure out why it’s not working for you.
If you heavily rely on containers cockpit probably also works better for you, though I’d also softly suggest thinking about using NixOS modules instead of containers, if this is an option for your infrastructure.