As far as the PnP goes, the Sage FAQ has this to say:
QuestionAnswer: 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.