As far as the PnP goes, the Sage FAQ has this to say:
Question: I can’t find any information about how many spells prestige class spellcasters know. I am going on the presumption that those that gain bonus spells per day of their existing class (such as loremaster and spellsword) do not automatically add additional spells to their spellbook as they gain levels.
Answer: They do add spells to their lists. For example, a wizard/loremaster gains 2 spells for her spellbook when using a loremaster level to increase spellcasting. A sorcerer/loremaster would learn more spells as well. Adding spells to your spellbook or personal repertoire is part of spellcasting.
But some people contend that the bonus 2 spells per class level are a class feature of the Wizard, listed under the Spellbooks section rather than in its own. A search on the topic has some people mentioning an official WotC prestige class that agrees that you don't get the two spells, and I believe I've read that too. Master Specialist, on the other hand, says you get the two spells as normal.
As far as NWN and the PRC goes, I -think- it's an engine limitation rather than a conscious decision based on any of the above.
