Not a problem in practice. I've seen a lot of systems having user homes in places other than /home for various (usually historical) reasons. Never broke anything afaik.
I've seen scripts with hardcoded "/home/$username" so your worries aren't entirely unfounded.
It's understandable too, because Linux doesn't provide a nice way to retrieve that information. You'll have to parse /etc/passwd (which might not contain all users) or hope that whatever language you're using supports path extrapolations so that you can do realpath(~username) or call a third party tool that does, like a shell.
Of course there is a nice way. 'getent passwd' if you have a shell script, or the getpwent() libc function if you are in some real programming language somewhere. That is ages-old POSIX stuff from almost the last century even (POSIX.1-2001, actually older than the standard even, since it has been in SystemV and BSD...), and Linux has always supported that.
