Preheat oven to 350 degrees F. First, make your honey syrup: In a small saucepan, combine the granulated sugar, lemon juice, water, and honey over medium-high heat. Bring to a boil, stirring until sugar dissolves, and then reduce heat to a simmer. Simmer for 4 minutes without stirring. Remove from heat and let cool while you prepare the baklava bites.
Line a rimmed baking sheet with foil for easier cleanup and lightly grease with foil. Arrange the phyllo shells onto the baking sheet in an even layer. Set aside.
Meanwhile, in a small bowl, combine the finely chopped nuts, cinnamon, and melted butter and stir until the melted butter has moistened the nuts and everything has combined. Using a cookie dough scoop, portion out the nut mixture into each phyllo cup, filling to the top. Compact the nut mixture into each cup using the back of the cookie dough scoop very gently.
Bake the baklava cups for 10 minutes. Remove from the oven and immediately disperse the honey syrup among the phyllo cups, about 1 teaspoon per baklava bite. If any leftover syrup remains, add an additional 1/2 teaspoon of syrup to each baklava bite until you run out of syrup.
Allow the baklava bites to cool completely, then allow them to set overnight so the flavors have a chance to meld together. (Pro tip: save the phyllo cup packaging and store the baklava in the phyllo cup holders within the package!). Let stand overnight.