The Hoshidan Royal family isn't directly related to the player in any form, which is why you can marry them. It reveals this in their S supports, and I'm assuming the player was brought at a very young age whereby Takumi and Sakura were born but very young.
Although Azura and Shigure are related to the player as first and second cousins respectively, it is actually legal to marry a cousin. so even if we find it weird, it's perfectly legal.
If Takumi and Sakura ARE related to you then...idk. I think in ancient Japan siblings would marry to "preserve bloodlines" which could be why, but I don't think Nintendo would allow incest.