Preheat oven to 350 degrees with rack in lower third. Rinse and dry ham and wrap first in parchment, then in foil, making sure thicker rind faces up. Place on a wire rack set in a rimmed baking sheet or roasting pan and bake 1 1/2 hours.
Meanwhile, stir together 1/3 cup horseradish, honey, allspice, 1/2 teaspoon salt, and 1/2 teaspoon pepper in a small bowl and set aside.
Remove ham from oven and unwrap. When cool enough to handle, peel rind from ham with a paring knife, trimming fat all over to about 1/2 inch. (It doesn't need to be perfectly even; the bottom will have less fat and more skin.) Pat dry. With the tip of the knife, score the skin with 1/4-inch-deep parallel lines, 1 to 2 inches apart. Then score skin in the opposite direction to create a diamond pattern. Return to oven and bake 30 minutes. Baste with honey-horseradish mixture and continue to bake, basting every 30 minutes, until a thermometer inserted into thickest part of flesh near (but not touching) bone registers 145 degrees, about 2 hours more. If necessary, add water to pan, about 1/4 cup at a time, to prevent pan from scorching, and tent with foil if ham begins to blacken.
Meanwhile, stir together creme fraiche, remaining 1/3 cup horseradish, thyme, and shallot. Season with 1 teaspoon salt and 1/2 teaspoon pepper. Transfer ham to a serving platter and let rest at least 20 minutes. Serve with horseradish cream.
Horseradish cream can be made up to 8 hours ahead and refrigerated; bring to room temperature before serving.