What issue do symlinks have that makes them worth listing as a negative? Asking as someone who wrote an installer script to make symlinks a decade ago, and has used it whenever setting up a new computer ever since.
I use them and have no issues, but some editors don’t respect symlinks when making backups when you’ve opened the symlink (Rename existing file, make new file with the old name, and now the symlink is renamed and subsequent updates are unlinked as well). I seem to recall I had to set an emacs var to avoid this behavior.
Flatpaks can be an issue depending on the sandboxing. The application may be restricted from accessing the target. Using a hardlinks works, so it isn't that big of an issue to have a couple hardlinks, but it is still something to keep in mind.
Enabling/disabling systemd services is done via managing symlinks. Unfortunately, when disabling a service in systemd, it follows and remove symlinks which can remove your symlinked service files.