The technical manuals aren't canon... and to be honest, it doesn't correspond with on-screen/canon data on technology in question.
From what we observed on-screen, the upper end yields for early TNG photon torpedoes seemed to have been in 500 megaton range.
Later on near the end of TNG and also in DS9 we say gigaton ranges.
If you take into account exponential developments in science and technology from the real world, it stands to reason the weapons would be much more powerful nearing the start of the Dominion War, and also by the end of the said war.
In fact, by mid-late TNG, we saw that the Enterprise-D was using a low charge and tightly focused phaser beam to drill into the planets crust... estimated yields were calculated to be about 1.5% of the total phaser output (which would require low gigaton yields).
At maximum, we've seen teraton level outputs (which are not inconsistent with the other shows) coming from Federation, Klingon, Romulan and Cardassian ships in DS9 for example.
Weapons also have excessively long range... phasers in TNG were seen to have at least 150 000 km range, and torpedoes 300 000 km ranges... for the Nebula class.
If the Enterprise-D was remotely comparable (and it stands to reason it was), we need to keep in mind it received upgrades to its shields and weapons which among other things extended their range (and likely firepower).
Furthermore, the 64 megaton yields for photon torpedoes are more in line with Kirk's era (TOS and Enterprise-A).