The magic books that grant inherent bonuses still grant bonuses, and an inherent bonus works just like any other bonus except it applies "to an ability score [and] results from powerful magic, such as a wish spell. A character is limited to a total inherent bonus of +5 to any ability score" (DMG 21). Also, the wish spell has some additional rules that explain how multiple wishes in rapid succession can be used to gain larger inherent bonuses.
Thus, like most other bonuses, inherent bonuses don't typically stack. So, for example, reading a second manual of gainful exercise +1—even simultaneously—provides the reader with the same +1 inherent bonus as a lone manual does. Want a bigger inherent bonus? Buy, create, or find a manual or tome that grants a bigger bonus. (Or find a way to use in a row more wishes.)
It's rare when any published stat block explains how a creature's ability scores are derived: the Monster Manual provides the creature's original ability scores before racial adjustments if those ability scores aren't all 10s and 11s (like if the NPC has levels in an NPC class), and NPCs that take levels in non-NPC classes get the elite array, but the game relies on the reader doing the math to derive a creature's original statistics if items have provided bonuses—if the reader needs to know the frost giant jarl's Charisma score absent its cloak of charisma +2 (Monster Manual 122-3), the reader must do that math himself: that bonus is already included in his stat block for convenience… despite neither Monster Manual nor individual monster description saying that's the case nor including entries like Cha 18 (includes the +2 enhancement bonus from the cloak of charisma +2 and a +1 ability score increase from increased Hit Dice). (I suspect this is because such notes, while useful for PCs, aren't that useful for a monster that'll only be on the board for 30 minutes or whatever and such notes occupy a lot of page space!)
However, the game does seem to make it clear that it's important for the reader to know when a creature's benefited from manuals and tomes: the pregenerated NPCs have listed among their possessions tomes and manuals marked as used in Bastion of Broken Souls (48), the level 20 high priest has among his possessions an already-read tome of understanding in the Dungeon Master's Guide II (166), and the elder orb Kularkuthan in Lords of Madness "has read a tome of leadership and influence +5; his +5 inherent bonus to Charisma is included in [his] statistics block" (43). These aren't the only examples—there are many more. A similar note should be made on the character sheet of any PC that likewise consumes a tome or manual.