The reason you limit the number of inodes a user can access is so they don't make the system as a whole run out of inodes by creating a huge number of 0-byte files.
With most Linux file systems (e.g. ext3 and ext4), each file (including device files) or directory has an inode -- a number used to point to a given file/directory. If a system runs out of inodes, it doesn't matter how much free space the hard disk has; it's impossible to make a new file until inodes are freed up.
To see how many inodes each filesystem has left:
df -i
The number of inodes a filesystem has is determined by the -i argument when formatting the file system. Examples:
mkfs -t ext4 -i 1024 /dev/foo # One inode per 1024 bytes
mkfs -t ext4 -i 2048 /dev/foo # One inode per 2048 bytes
mkfs -t ext4 -i 8192 /dev/foo # One inode per 8192 bytes
The filesystem created with the -i 1024 option will have eight times as many inodes as the filesystem created with the -i 8192 option (assuming both file sytems are the same size). Sometimes, especially with some mail servers (that use "maildir") or old-school Usenet spools, one needs more inodes, since those use cases create a lot of small files.
Note that some Linux filesystems, such as Reiserfs, are able to dynamically assign inodes and do not create all of them at filesystem creation time.
