Why can't files be manipulated by inode?

Security reasons -- to access a file you need permission on the file AS WELL AS permission to search all the directories from the root needed to get at the file. If you could access a file by inode, you could bypass the checks on the containing directories.

This allows you to create a file that can be accessed by a set of users (or a set of groups) and not anyone else -- create directories that are only accessable by the the users (one dir per user), and then hard-link the file into all of those directories -- the file itself is accessable by anyone, but can only actually be accessed by someone who has search permissions on one of the directories it is linked into.

Some Operating Systems do have that facility. For example, OS X needs it to support the Carbon File Manager, and on Linux you can use debugfs. Of course, you can do it on any UNIX from the command-line via find -inum, but the real reason you can't access files by inode is that it isn't particularly useful. It does kindof circumvent file permissions, because if there's a file you can read in a folder you can't read or execute, then opening the inode lets you discover it.

The reason it isn't very useful is that you need to find an inode number via a *stat() call, at which point you already have the filename (or an open fd)...or you need to guess the inum.

In response to your comment: To "pass a file", you can use fd passing over AF_LOCAL sockets by means of SCM_RIGHTS (see man 7 unix).