The Apple command-line tool is exactly the same as Linux. What I do not personally know is what shell options you have on Apple. I used bash on Linux and I could provide some examples using bash, if that helps.
AES Crypt does not encrypt directories. It only encrypts files. If you wish to encrypt an entire directory and all of its sub-directories, I would suggest you use a tool like "tar" to archive the files. Something like this:
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$ tar -czf /path/to/archive.tgz input_folder_name
$ aescrypt -e /path/to/archive.tgz
$ rm /path/to/archive.tgz
This will create a compressed archive of the folder, you then encrypt it, and remove it. You can do this all in one step:
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$ tar -czf - input_folder | aescrypt -e -p apple -o /path/to/archive.tgz.aes -
Note the - characters. This tells the shell to take input as standard input. Basically, it allows data to be piped right out of one program and into another. I use this technique to backup and encrypt folders on my own machines. (The one thing I do not like is putting the password on the command-line, so at some point we will introduce a -k option to allow reading the encryption key from a file.)
If you have a folder and you want to encrypt each file in it as a separate .aes file, you can do that. However, I've found that to be a bit messy to deal with. It's really much cleaner to create one large archive file. But, if you really want to do that, we could create a shell script that does that. This is the "UNIX way" of doing things. AES Crypt just becomes one tool in the chain