That portion of the rules should answer the majority of your first question. They cost more because they are more customizable in terms of skills than other NPCs. At the moment they are not much use, however, since they can't perform any specific functions.
2) The majority of stocks make no profit; very few factions pay their shareholders, and those that do so generally strike some deal with them in advance where the shareholder needs to purchase some given quantity of shares before he will receive any dividends. They are generally just collected since they allow you to acquire basic information on a faction. The prices don't actually fluctuate a whole lot, and are primarily based on the rarity of the stock.