One of the selling points of git-annex is that it uses standard tools like git and gpg to deal with files, so that years from now it should be possible to explore and get useful data out of an old annex repository (this helps with future proofing). If for whatever reason you need to decrypt files on special remotes that use encryption without using git-annex, this can be done fairly easily using gpg (and openssl to compute the HMAC keys used to create the file names used on the special remote so you can look up the right file to decrypt). Here is an example script demonstrating how to compute the special remote file names and how to decrypt the special remote files.

#!/usr/bin/env bash

usage() {
    echo "Usage: ga_decrypt.sh -r REMOTE [-k SYMLINK] [-d FILE]"
    echo ""
    echo "    Either lookups up key on REMOTE for annex file linked with SYMLINK"
    echo "    or decrypts FILE encrypted for REMOTE."
    echo ""
    echo "    -r: REMOTE is special remote to use"
    echo "    -k: SYMLINK is symlink in annex to print encrypted special remote key for"
    echo "    -d: FILE is path to special remote file to decrypt to STDOUT"
    echo ""
    echo "NOTES: "
    echo "    * Run in an indirect git annex repo."
    echo "    * Must specify -k or -d."
    echo "    * -k prints the key including the leading directory names used for a "
    echo "       directory remote (even if REMOTE is not a directory remote)"
    echo "    * -d works on a locally accessible file. It does not fetch a remote file"
    echo "    * Must have gpg and openssl"
}

decrypt_cipher() {
    cipher="$1"
    echo "$(echo -n "$cipher" | base64 -d | gpg --decrypt --quiet)"
}

lookup_key() {
    encryption="$1"
    cipher="$2"
    symlink="$3"

    if [ "$encryption" == "hybrid" ] || [ "$encryption" == "pubkey" ]; then
        cipher="$(decrypt_cipher "$cipher")"
    fi

    # Pull out MAC cipher from beginning of cipher
    if [ "$encryption" = "hybrid" ] ; then
        cipher="$(echo -n "$cipher" | head  -c 256 )"
    elif [ "$encryption" = "shared" ] ; then
        cipher="$(echo -n "$cipher" | base64 -d | tr -d '\n' | head  -c 256 )"
    elif [ "$encryption" = "pubkey" ] ; then
        # pubkey cipher includes a trailing newline which was stripped in
        # decrypt_cipher process substitution step above
        IFS= read -rd '' cipher < <( printf "$cipher\n" )
    fi

    annex_key="$(basename "$(readlink "$symlink")")"
    hash="$(echo -n "$annex_key" | openssl dgst -sha1 -hmac "$cipher" | sed 's/(stdin)= //')"
    key="GPGHMACSHA1--$hash"
    checksum="$(echo -n $key | md5sum)"
    echo "${checksum:0:3}/${checksum:3:3}/$key"
}

decrypt_file() {
    encryption="$1"
    cipher="$2"
    file_path="$3"

    if [ "$encryption" = "pubkey" ] ; then
        gpg --quiet --decrypt "${file_path}"
    else
        if [ "$encryption" = "hybrid" ] ; then
            cipher="$(decrypt_cipher "$cipher" | tail -c +257)"
        elif [ "$encryption" = "shared" ] ; then
            cipher="$(echo -n "$cipher" | base64 -d | tr -d '\n' | tail  -c +257 )"
        fi
        gpg --quiet --batch --passphrase "$cipher" --output - "${file_path}"
    fi
}

main() {
    OPTIND=1

    mode=""
    remote=""

    while getopts "r:k:d:" opt; do
        case "$opt" in
            r)  remote="$OPTARG"
                ;;
            k)  if [ -z "$mode" ] ; then
                    mode="lookup key"
                else
                    usage
                    exit 2
                fi
                symlink="$OPTARG"
                ;;
            d)  if [ -z "$mode" ] ; then
                    mode="decrypt file"
                else
                    usage
                    exit 2
                fi
                file_path="$OPTARG"
                ;;
        esac
    done

    if [ -z "$mode" ] || [ -z "$remote" ] ; then
        usage
        exit 2
    fi

    shift $((OPTIND-1))

    # Pull out config for desired remote name
    remote_config="$(git show git-annex:remote.log | grep 'name='"$remote ")"

    # Get encryption type and cipher from config
    encryption="$(echo "$remote_config" | grep -oP 'encryption\=.*? ' | tr -d ' \n' | sed 's/encryption=//')"
    cipher="$(echo "$remote_config" | grep -oP 'cipher\=.*? ' | tr -d ' \n' | sed 's/cipher=//')"

    if [ "$mode" = "lookup key" ] ; then
        lookup_key "$encryption" "$cipher" "$symlink"
    elif [ "$mode" = "decrypt file" ] ; then
        decrypt_file "$encryption" "$cipher" "${file_path}"
    fi
}

main "$@"