This AppleScript will get the total word counts of a folder of ID files—it shouldn't be too hard to convert to JavaScript if you are not using OSX:
tell application "Finder"
activate
set myFolder to choose folder with prompt "Select the folder containing the files to count"
set myFiles to every file of folder myFolder whose file type is "IDd5"
end tell
tell application "Adobe InDesign CS3"
set wordcounts to {}
set total to 0
repeat with j from 1 to (number of items in myFiles)
open item j of myFiles
tell active document
tell every story
set wordcounts to wordcounts & (count every word)
end tell
set totalstories to count every item of wordcounts
repeat with i from 1 to totalstories
set total to total + (item i of wordcounts)
end repeat
close
end tell
end repeat
display dialog "The documents in the selected folder have a total of " & totalstories & " stories, and " & total & " words"
end tell
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If you just want the active document's count it would be:
tell application "Adobe InDesign CS3"
tell active document
set wordcounts to {}
tell every story
set wordcounts to wordcounts & (count every word)
end tell
set total to 0
set totalstories to count every item of wordcounts
repeat with i from 1 to totalstories
set total to total + (item i of wordcounts)
end repeat
display dialog "Total words in all " & totalstories & " stories: " & total
end tell
end tell
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