Thinly slice the cucumbers into 1/8-inch rounds and very thinly slice the red onion into half-moons. Uniform thin slicing is important here because it allows the vegetables to absorb the dressing evenly and creates a pleasant texture throughout the salad. Set the prepared vegetables aside in a large mixing bowl.
In a small bowl or measuring cup, whisk together the apple cider vinegar, honey, and salt until the honey is fully dissolved and the salt is incorporated. Pour this mixture over the sliced cucumbers and onions, then toss everything together until well coated. The salt will begin drawing out the cucumber's natural liquid, which will mingle with the vinegar to create a light brine. I like to taste the dressing at this stage and adjust the salt or vinegar if needed before chilling.
Refrigerate the cucumber mixture for at least 20 minutes to allow the flavors to meld and the vegetables to soften slightly. After chilling, strain the salad through a colander or fine-mesh strainer, reserving about 2-3 tablespoons of the accumulated liquid but discarding most of it—this prevents the salad from becoming watery as it sits. I find that draining the excess liquid is key to keeping the salad crisp and flavorful rather than soggy.
Transfer the drained cucumber salad to a serving bowl. Drizzle the extra-virgin olive oil over the top and toss gently to coat. Scatter the fresh dill and chives across the salad, then season generously with freshly ground black pepper and a pinch of red pepper flakes for a subtle heat. Toss one final time just before serving to distribute the herbs and seasonings evenly.