I don’t know how much this varies by distro, but I find the updates completely non intrusive. I think in Fedora I’ve seen one or two “critical updates are available” or “version N+1 is available” popups, but they aren’t intrusive and don’t get in the way. I’m not sure if I’ve seen a popup in Mint or not. Most of the time I notice there’s an update available because there’s a notification in the system tray or equivalent.
And I’m not even here to bash how Windows does it. I haven’t had many issues with my windows machines because I’ll check for updates and/or install available ones right away. Either that or I don’t use the machine for a while (working as a server) and it may or may not restart itself at night sometimes.
I still prefer the Linux way, which is kind of a win-win in my eyes because you get control over updates and reboots AND your system isn’t as much of a target in the first place so updates aren’t usually time critical.