For apache, or any user/process to have access to a user's ecryptfs-encrypted home directory, the encrypted directory must be mounted. During login, mount.ecryptfs_private is used to mount the encrypted volume - the user's password being used to obtain the key to decrypt the volume. If the user isn't logged on, then you can script the mounting of the user home directories with ecryptfs-mount-private.
I've found references that say it's possible to automount volumes encrypted with ecryptfs utilities, but nothing that explains how to actually do it. If you really need encryption for all home directories, but want a system process to have access to them, you might want to consider implementing block-level encryption with dm-crypt or something else. Check out the /usr/share/doc/ecryptfs-utils/ecryptfs-faq.html file on your server and https://help.ubuntu.com/community/EncryptedHome for more information.
Lastly, deciding whether or not you need to encrypt data residing on disk is completely your choice - if you're concerned about the confidentiality of the data, then encryption is one of several tools you can use to protect it. The best security comes from evaluating your options and implementing a multi-tiered approach that fits your business needs - firewalls, patch management, ACLs, physical access, encryption...