Here's a AppleScript that will do it. It saves as Acro6 with layers, no AI editability, and embedded fonts. Copy and paste into the Apple Script Editor, compile and save into HD>Applications>Adobe Illustrator>Presets>Scripts.
-- fileList is a list of aliases to Illustrator files
-- destFolder is an alias to a folder where PDF files are saved
on SaveFilesAsPDF(fileList, destFolder)
set destPath to destFolder as Unicode text
repeat with aFile in fileList
tell application "Finder" to set fileName to name of aFile
set newFilePath to destPath & fileName
tell application "Adobe Illustrator"
open aFile
save current document in file newFilePath as pdf with options {class:PDF save options, acrobat layers:true, compatibility:Acrobat 6, preserve editability:false, font subset threshold:0.0}
close current document saving no
end tell
end repeat
end SaveFilesAsPDF
-- Call handler
set sourceFolder to choose folder with prompt "Source folder?"
tell application "Finder" to set fileList to every file of folder sourceFolder as alias list
set destFolder to choose folder with prompt "Destination folder?"
SaveFilesAsPDF(fileList, destFolder)