The encrypted home utilities don't support the ability to enable encrypted filenames after you've set up your encrypted home directory. But, I looked at the ecryptfs-migrate-home script and believe that it should be enabling filename encryption by default.
Let's verify that filename encryption is enabled. Do you have two lines in your key signature file?
$ wc -l ~/.ecryptfs/Private.sig
wc reports that there are two lines, things are looking good so far. Check to see if the eCryptfs mount includes the filename encryption key signature mount option:
$ grep ecryptfs_fnek_sig= /proc/mounts
/home/user/.Private /home/user ecryptfs rw,nosuid,nodev,relatime,ecryptfs_fnek_sig=0011223344556677,ecryptfs_sig=8899aabbccddeeff,ecryptfs_cipher=aes,ecryptfs_key_bytes=16,ecryptfs_unlink_sigs 0 0
If you see the ecryptfs_fnek_sig option, things are looking even better. Now make sure that filenames are encrypted in the lower filesystem:
$ ls /home/.ecryptfs/user/.Private
Do all filenames have a "ECRYPTFS_FNEK_ENCRYPTED." prefix? If so, the filename encryption feature is configured and working correctly.