Is this a fan-forced application or natural convection? If the latter, then make sure you mount the heat sink with fins vertically. As to your question, if this is natural convection, then you shouldn't lost much cooling with the alternate design. If it's fan-forced, then that depends upon where the fan is mounted (and for fan-forced a lot of lower but more densely packed fins would be better).
What J_C said. It probably makes a big difference. The scale of your drawing is also important. You may not need the entire length of the fins anyway. You might be able to use more, and shorter, fins. But it's unlikely.