chflags nohidden does not seem to work in macOS Mojave.
It works fine in OS X 10.10.5.
Is it a problem specific to macOS Mojave or is it related to the fact that the volume is a APFS one?
Also I'm not sure to understand why when you open an invisible PNG and export it as-is with Preview.app, the exported image is still invisible. It's supposed to be an export, not a duplicate.
I'm having the same issue and have found no solutions. Have you had any luck since?
Same error in the current release version ! 10.14.2 (18C54)
ACTUAL SOLUTION:
It requires two lines being typed into terminal.
1.) Open terminal and type the following and hit enter
xattr -d com.apple.FinderInfo ~/Library
2.) Type this additional line and hit enter.
chflags nohidden ~/Library
Your library folder should now be visible!