Just to confirm, the Moriya in Mononobe no Moriya has absolutely no relations to the Moriya in Moriya Suwako or whatever it was based on, and is a simple coincidence, right?
It's just a coincidence. Mononobe no Moriya's name is written 守屋, while the Moriya god/Suwako is 洩矢.
The Moriya Shrine in real life is 洩矢神社, while the Touhou version is 守矢神社. ZUN changed one character, simply to differentiate the fictional shrine (which hosts both Kanako and Suwako) from reality.
Huh, I knew I forgot something important. While in real life the Moriya god and shrine are both 洩矢, their priest family is called 守矢. The Moriya clan is by tradition descendants of the Moriya god, and very likely the ancient rulers of the Suwa region, before they were conquered by the Yamato people (mirrored in the mythology of Take-Minakata and the Moriya god). In fact, Sanae's given name is taken from the Moriya family's current matriarch, 守矢早苗,
The real life Sanae Moriya, 78th generation leader of the Moriya clan
As an interesting side note, according to
one Wikipedia article on a certain Moriya priest of the 16th century, there actually had been a rumour in history that the Moriya clan was descended from Mononobe no Moriya, whose family members might have changed their names to escape persecution. So the medieval Japanese noticed this coincidence too.