there has been no offical answer on this obviously, however it's possiable these technologies where destroyed to limit the breach of the temporal prime directive Since the Enterprise-E didn't have them in 2379, probably not. They were either confiscated by Temporal Investigations shortly after Voyager's return, or the systems weren't being rolled out very quickly.
Transphasic torpedoes weren't used unless there was a Borg invasion. Transphasic torpedoes and ablative generators wouldn't become practical until the 25th century, when they were invented and ready to use.
What is this? Photon Torpedoes: The Next Generation ?