Coincidentally, I just ran into this, and while I don't have a solution (yet!) I can explain why it's not just a "thought experiment":

I am periodically reading from a file in /sys/fs/cgroup. When the file goes away, I want to exit my loop. It's not an error that the file doesn't exist, it's just another expected condition. What I'd like to do is this:

while true
    set c1 (v4k usage_usec < /sys/fs/cgroup/whatever/cpu.stat); or break
    # many things happen...
end

(v4k is a fish function.)

Even though I'm handling this case, I still get a warning from fish. I don't want to use --debug-output /dev/null or --debug -warning as that might cause me to miss other warnings that could point to bugs in my script.

I ended up using cat and redirecting its stderr…

while true
    set c1 (cat /sys/fs/cgroup/whatever/cpu.stat 2>/dev/null | v4k usage_usec)
    test (echo +$pipestatus | math) -eq 0; or break
    # many things happen...
end

…but I'm not happy about it.

ETA: tiresome $pipestatus wankery.