Yes, even if a pond liner is eventually covered by rocks, UV damage can begin during installation. Once molecular damage begins, it continues, unseen, even if the sun never reaches the liner again. Even with an expensive border of rocks, though, the waterline continues to be a liner's most vulnerable spot.
The best defense against UV damage is a liner that's engineered for UV resistance. EPDM is naturally UV-resistant but it's vulnerable to other types of weathering. Reinforced Polyethylene contains carbon black, a powerful UV absorber and stabilizer, which significantly increases your liner's lifespan.
