Place racks in the upper and lower thirds of your oven and preheat to 375 degrees F. Line two standard-sized 12-cup muffin tins with paper liners and place 1 gingersnap in the bottom of each.
In the bowl of a standing mixer fitted with the paddle attachment or a large mixing bowl, beat the cream cheese on medium speed until smooth and fluffy, about 2 minutes. Scrape down the bowl, then beat in the sugar for 1 to 2 minutes more, until the mixture looks smooth and shiny.
Scrape down the bowl, then beat in the eggs, 1 at a time, being sure to fully incorporate between each. Scrape down the bowl again as needed.
Beat in the pumpkin, Greek yogurt, pumpkin pie spice, cinnamon, vanilla, salt, and orange zest, stopping to scrape down the bowl as needed.
With an ice cream or cookie scoop or a small ladle, fill each muffin cup nearly to the top with batter, dividing it evenly between the 24 cups (the cheesecakes will settle as they cool).
Bake the mini cheesecakes for 18 to 20 minutes, rotating the pans 180 degrees and switching their positions on the upper/lower racks halfway through. When the pan is wiggled, they should move slightly in the very center (like Jello, not like a wave). The edges of the cheesecakes should appear dry and set and not move when you wiggle the pan.
Place the pans on a wire rack and let cheesecakes cool in the pan for at least 1 hour. Gently transfer them to a plate or storage container. Refrigerate for 4 hours (uncovered) or overnight (covered) to set.
When ready to serve, top each cheesecake with whipped cream, pecans, and a sprinkle of crushed gingersnaps.
TO STORE: Refrigerate cheesecakes in an airtight storage container for up to 1 week.
TO FREEZE: Freeze leftovers in an airtight, freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before serving.