Null value is eliminated by an aggregate or other SET operation - warning also whan NULLs changed by 0

Should I see this warning when I have ISNULL check at SUM function and changing NULLs to 0?

If this setting is ON, then yes:

It's a harmless warning for the circumstance you're seeing, and since this setting has other effects it's better to leave it on.

When using SUM(), you don't need to change NULLs to 0 as they will simply be ignored.

The fact you're trying to replace them with 0 and are still getting the warning tells me something is being overlooked, but rather than try to determine what that could be... I recommend just removing the ISNULL(), as it is unnecessary.