Trim off about 1/2 inch from each end of squash; discard. Slice remaining midsection of squash crosswise into 4 (3/4-inch-thick) rounds. Remove seeds and membrane with a spoon.
Brush both sides of squash with oil, and place on a baking sheet coated with cooking spray. Sprinkle with 1/4 teaspoon salt and crushed red pepper. Bake at 425° for 15 minutes or until squash is just fork tender.
Remove baking sheet from oven. Crack an egg into the center of each acorn slice; sprinkle eggs with remaining 1/8 teaspoon salt. Return pan to oven, reduce oven temperature to 350° and bake for 12 minutes or until eggs are cooked. Transfer to plates using a wide spatula; sprinkle with thyme and bacon. Serve immediately.