MergeSOP effectively creates new geometry object consisting of primitives of its inputs. Houdini can usually avoid actual copy, but I suspect that depending on a state of input geometry it might be forced to do even more. Copying attribute requires hardening it, which means baking all intermediate stages, removing holes, sorting etc. It can take a while. I don't know how Houdini handles copying packed prims, but it might be yet another story.
Whatever it your case, you shouldn't merge geometry for rendering. People usually do the opposite: so even if peaces are kept together for some reason (like sim), they are at the very end separated into many objects for rendering. It's cleaner and easier to handle, it's better performance-wise both for exporting to renderer and for rendering itself.