Are freckles a sign that the skin has been damaged by the sun?

Yes. When the tendency to form freckles can be hereditary, freckles themselves are a sign of damage from uv rays. Some people are more prone to develop freckles (red heads, celtic background, fair skin, etc) but they can minimize them by stay out of the sun and using strict sun protection. Just look at someone's bottom which are often freckle free since the sun never shines there!
Not necessarily. Most freckles are inherited from family members. Freckles may increase with sun exposure, which could indicate sun damage. Also people with freckles often have fair skin, which makes them more sensitive to sun damage.
Sometimes. Freckles or lentigenes can be inherited or acquired. In acquired, they are generally harmless and not associated with any systemic disorders. Indeed, the more sun exposure/damage you've had, the more lentigenes become apparent in adulthood, commonly called "sun spots". Examples of inherited syndromes that are associated with freckling are neurofibromatosis 1 and multiple lentigenes syndrome.