Here's the annex-du script that I use:

#!/bin/sh
git annex find "$@" --include '*' --format='${bytesize}\n' |awk '{ sum += $1; nfiles++; } END { printf "%d files, %.3f MB\n", nfiles, sum/1000000 } '

This one can be slow on a large number of files, but it has an advantage of being able to use all of the filtering available in git annex find.
For example, to figure out how much is stored in remote X, do

annex-du --in=X
