We do both depending on our goals. If it's a lead gen email, we use programs so that we can measure the outcome of each send. In which case, the entire program (including the smart campaign) is cloned.
But for client communications we will re-use the smart campaign to cut down on the smart campaign clutter. However, I do clone them and start fresh once a year so that one smart campaign doesn't get too full of data. That could eventually slow you down.