I imagine it doesn't distinguish between @reply's and normal messages. I'm making this assumption because it assigned me a Shuush level of 5 even though nearly all of my tweets are @reply's, but other people who tweet "regular" tweets far more often than me were assigned 3's and 4's. I wouldn't be surprised if all it's really doing is taking the two data points of number of tweets and signup date and using that to compute an average tweets-per-day metric.