Perhaps we're thinking about this wrong. Sure, the Intrepid class' top speed is Warp 9.975, but it doesn't sustain that speed forever. Someone worked out that Voyager's 70 year journey was actually based on a speed around Warp 6 or something, far less than top speed. In aircraft design, military jets in particular, they are designed with an efficient cruise speed and a dash speed, which is the top (although unsustainable and inefficient) speed. Maybe the Nova class' engines, due to it only being a survey ship, is only capable of cruise speed, and not a dash speed. In that regard, the Nova class would likely matches the Intrepid class' cruise speed, which is what it would be traveling at most of the time anyway.