You do not mount directories. Directories are files.
eCryptfs has to work as a layer on top of another filesystem.
When you mount eCryptfs over a directory, it decrypts the files in it... allowing plain-text access.
overview of concepts
including dicussions of the sorts of security issues that ecryptfs is supposed to solve.
You can get ecryptfs "partitions" to mount at boot easily enough:
... the approach is to mount the partition fs first, then mount ecryptfs over the top of that.
presumably you can do something similar for hotpluggable devices in the udev rules.
Cannot see any reason you cannot have more than one ecryptfs encrypted directory. Easy to check. Try it and see.