Both are beautiful, but they offer very different kinds of romance, so the answer really depends on what kind of honeymoon you're after.
Shimla feels colonial, cozy, and walkable. Mall Road at dusk, the Ridge at sunrise, quiet cafés, and a slower pace. If you want to hold hands and stroll without renting a vehicle every day, Shimla wins. It's elegant in an old-world way.
Manali is more adventurous and raw. Solang Valley, Rohtang (if it's open), riverside stays in Old Manali, the smell of pine for