User input in Automator's "Run Shell Script"
Using display notification will be of no use since its result is none, use a display dialog instead.

The follow is an example of how I'd do it:

result="$(osascript -e '(display dialog "Do you want to Rsync now?" buttons {"No", "Yes"} default button 2 with title "ssh")')"
if [ "$result" == "button returned:Yes" ]; then
    rsync -czvaEP --delete --log-file=$log "$source" -e "ssh -p$port" $user@$host:$path;
fi




Shown within the relevant code posted in the OP:

source="/Volumes/MyDisk/FolderToSync"

user="username"
host="myhost"
port="22"
path="/RemoteFolder/"

log="$HOME/RSync_$(date +%Y.%m.%d_%H-%M-%S).log"
rm $HOME/RSync_$(date -v-1m +%Y.%m.)*.log

if [ -d "$source" ]; then

    nc -z $host $port &gt; /dev/null   

    if [ $? -eq 0 ]; then
        touch $log;
        result="$(osascript -e '(display dialog "Do you want to Rsync now?" buttons {"No", "Yes"} default button 2 with title "ssh")')"
        if [ "$result" == "button returned:Yes" ]; then
            rsync -czvaEP --delete --log-file=$log "$source" -e "ssh -p$port" $user@$host:$path;
        fi
    fi
fi