Preheat oven to 425°.
Cut each squash in half lengthwise; discard seeds and membranes. Place squash, cut sides down, on a jelly-roll pan coated with cooking spray.
Combine onion and oil, tossing to coat. Spread onion mixture onto pan around squash. Bake at 425° for 45 minutes or until squash and onion are tender. Cool slightly. Scoop out squash pulp from skins; discard skins.
Place onion and squash pulp in a Dutch oven. Stir in broth and the next 5 ingredients (through pepper); bring to a boil. Reduce heat; simmer 5 minutes.
Place half of squash mixture in a blender. Remove center piece of blender lid (to allow steam to escape); secure blender lid on blender. Place a clean towel over opening in blender lid (to avoid splatters). Blend until smooth. Pour into a large bowl. Repeat procedure with remaining squash mixture. Return pureed mixture to pan; stir in half-and-half. Cook over medium heat 5 minutes or until thoroughly heated. Garnish with thyme, if desired.