The fact that they are not mentioned again does not necessarily mean that they were destroyed. Who knows if these big trees survived somewhere in the Far East or South...? (Ooh, maybe they transformed into giant elephants and became known as
műmakil in the later ages...
)
As to
Hookbill's Ent theory, it is cute, but it has its problems. As far as I know, Ents were of the size of normal trees, not giant trees and it seems unlikely that they would have become smaller in the process of developing a conscious mind and learning to speak and move.
Maybe they were originally, or became so when time passed, as hard as stone and very much like, indeed, maybe this explains the mystery of Orthanc. Maybe it was the last giganto-tree, transformed into a magnificient tower by the Gondorians. Maybe that's why the Ents took it so positively to guard Isengard.