Um pôster acima pediu que eu refizesse minha resposta como uma resposta real para a posteridade. Aqui está a resposta. Obrigado a todos pela vossa ajuda.
Eu respondi minha própria pergunta. Aqui está um script que parece fazer o truque. Eu gostaria de receber ajuda para avaliar porque o código que eu comentei não funciona ...
#!/bin/bash
# Created by Dave, 2012-02-23
# This script uses PDFtk to password protect every PDF file
# in the directory specified. The script creates a directory named "protected_[DATE]"
# to hold the password protected version of the files.
#
# I'm using the "user_pw" parameter,
# which means no one will be able to open or view the file without
# the password.
#
# PDFtk must be installed for this script to work.
#
# Usage: ./protect_with_pdftk.bsh [FILE(S)]
# [FILE(S)] can use wildcard expansion (e.g., *.pdf)
# This part isn't working.... ignore. The goal is to avoid errors if the
# directory to be created already exists by only attempting to create
# it if it doesn't exists
#
#TARGET_DIR="protected_$(date +%F)"
#if [ -d "$TARGET_DIR" ]
#then
#echo # echo "$TARGET_DIR directory exists!"
#else
#echo # echo "$TARGET_DIR directory does not exist!"
#fi
#
mkdir protected_$(date +%F)
for i in *pdf ; do pdftk "$i" output "./protected_$(date +%F)/$i" user_pw [PASSWORD]; done
echo "Complete. Output is in the directory: ./protected_$(date +%F)"