Reduce the oven temperature to 325°F (163°C). Bring a small pot of water to a boil.
In the bowl of a stand mixer or with a handheld mixer on medium speed, beat the cream cheese until fluffy and smooth, about 3 minutes. Beat in the sugar and vanilla, scraping down the sides of the bowl as needed.
Reduce the speed to low. Add the eggs, 1 at a time, beating well after each addition and scraping down the sides of the bowl as needed. Beat in the molasses, salt, ginger, cinnamon, nutmeg, cloves, and zest.
Scrape the filling onto the cooled gingerbread crust. Place the springform pan in a large, shallow roasting pan. Pull out the center oven rack and set the roasting pan on the rack. Carefully pour enough boiling water into the roasting pan to reach halfway up the side of the springform pan and then push the rack back into the oven.
Bake the cheesecake until the filling is an even, gorgeous pale shade of brown and appears set but is still slightly wobbly in the center, 60 to 70 minutes. (We had the best results when we took the cheesecake out at 65 minutes.) Transfer the springform pan to a wire rack and let the cheesecake cool completely. When the cheesecake has cooled to room temperature, slide it in the refrigerator, uncovered, and come back for it 8 hours later.
Before serving, run a knife or an offset spatula around the edge of the gingerbread cheesecake to loosen it from the sides of the pan. Carefully remove the pan and, if desired, arrange the gingerbread cookies around the center of the cheesecake.