The Yu Pagodas are there for practical reasons. During the Aeon fights (including Braska's FA), they dispel all status ailments, and heal for about 3000 HP (1500 each), AND they increase the Overdrives of the Aeons. Fortunately for you, none of the Aeons can break 9999, and even if you die, it's instant Auto-Life.

The Yu Pagodas themselves are more of an Enigma. They could be statues and reanimated, as other people have said. Also in the cutscene after Yu Yevon's defeat, they seal themselves and Yu Yevon away from the final encounter. They could be the guardians of an alternate dimension, but nothing more is said on the matter in the game, even if anyone knew of the existence of the Pagodas.