IloveEroge
As far as I understand the lore behind Megail's money, in chapter 1/2 Megail isn't fully on Team Simon yet, so she has some personal businesses to run. If you don't take the money, you get 200,000 ProN during Megail's route (which drops down to 150,000 ProN if you take the 25,000 ProN and 10,000 Sx) and 300,000 ProN in reunion (which drops down to 200,000 ProN if you take the money earlier).
Regarding Shining Swords, yes, they do play a role. Late game, like, really really really late game, a certain someone will be able to craft powerful equipment (as well as several key items) with them. We don't know how important they are or how much wiggle room there will be, though.