Just checked my disk:
peter@Zany:~$ locate '~' | wc -l
6314
So 6000+ files have a ~ in their path. Perhaps half of them are backup files. But clearly Apple uses them with paths like:
~/Library/Mobile Documents/iCloud~com~barebones~bbedit
~/Library/Dictionaries/CoreDataUbiquitySupport/ (lots of files with ~’s in them)
In any event, feel free to not use “~”, but there is no reason not to use it. It's really quite a useful file system character.