Be has reserved the /boot/beos/ directory (and its subdirectories) for its own applications, and strongly recommends against either putting other applications there or moving its contents around. If you want icons in that space for your own organizational reasons, drop symlinks into the directory, not actual applications.
While you’ll find that things will probably still work if you mess with this directory, don’t be surprised if changes you’ve made to this directory are overwritten the next time you install or upgrade the OS.
/boot/home/ and subdirectories are the recommended location for 3rd-party applications, though you’ll probabably want to create /boot/home/apps/