For the dough: Sprinkle the yeast over 1 1/2 cups warm water (not over 110 degrees F) and allow it to bloom. When it has bloomed, the mixture will bubble a bit.
In the bowl of a stand mixer fitted with a paddle attachment, combine the flour and salt. With the mixer running on low, drizzle in the olive oil and mix until combined. Pour in the yeast mixture and mix until a dough forms.
Drizzle roughly 2 tablespoons of olive oil in a medium bowl and coat the sides of the bowl with it. This will prevent the dough from sticking. Tip the dough into the oiled bowl, form a ball with it and gently coat it lightly with the residual olive oil on the sides. Cover the bowl tightly with plastic wrap and allow the dough to rise in a warm place until roughly double in size, at least 1 hour.
For the filling: Combine the cream cheese, Cheddar and ham in a large mixing bowl. Stir until well combined. Set aside.
For the everything bagel seasoning: Mix together the sesame seeds, poppy seeds, sea salt, onion flakes, garlic flakes and pepper in a small bowl. Set aside.
Preheat the oven to 425 degrees F. Add the honey and 10 cups water to a large pot and bring to a boil.
Once the dough has risen, divide it into 16 pieces. Roll each piece into a ball. Lightly flour a work surface and use a rolling pin to roll each ball into a 4-inch circle roughly 1/4 inch thick. Top each circle with 3 tablespoons of the filling. Pull the dough up and around the filling, pinching the seam at the top. Make sure you fully encase the filling. Place the finished bombs seam-side down on a greased baking sheet.
Add the bagel bombs to the boiling water in batches of 4; boil for 1 minute, flipping halfway through. Remove to a separate baking sheet and top each with a generous pinch of the everything bagel seasoning blend.
Once all of the balls of dough have been boiled, transfer them to another greased baking sheet and bake until golden brown, about 25 minutes. Enjoy!
Freezer Directions: Follow the steps above and allow the bagel bombs to cool completely after baking, roughly 45 minutes to 1 hour. Place in the freezer, uncovered, for 20 minutes. Remove and individually wrap each bomb in foil. Return them to the freezer to fully freeze.
When ready to eat, remove a bagel bomb (or more) from the freezer. Remove the foil and wrap the bomb in a paper towel. Microwave for 90 seconds or until cooked through. Allow it to sit for 1 minute before taking out of the microwave. Unwrap and enjoy!