Preheat the oven to 400 degrees F (200 degrees C). Grease 18 muffin cups or line cups with paper liners.
Whisk soy milk and apple cider vinegar together in a bowl. Set aside and allow to curdle to create "buttermilk", about 10 minutes.
Stir gluten-free flour, baking powder, baking soda, salt, and poppy seeds together in a separate bowl. Whisk together sugar, oil, and lemon zest together in a large bowl. Slowly stir in lemon juice, vanilla extract, and "buttermilk"-mixture. Add flour mixture and mix until batter is combined.
Spoon batter into the prepared muffin cups, filling each 2/3 full.
Bake in the preheated oven until tops spring back when lightly pressed and a toothpick inserted into the center of a muffin comes out clean, 18 to 20 minutes. Cool in tins for 5 minutes. Transfer to a wire rack to cool completely, 10 to 15 minutes.
While the muffins are cooling, whisk together confectioners sugar and 2 tablespoons lemon juice in a small bowl and create a smooth glaze. After the muffins have cooled, drizzle glaze on muffin tops.