Sanae can mean "rice seedling" or "early seedling", and Kotiya "eastern wind valley". (The same "east" as in Touhou, and the same "wind" as in Fuujinroku.)
In fact, there is an old lady named Sanae Moriya (守矢早苗), who is the 78th head of Moriya family. The family were supposed to succeed to one of the priests of the Suwa Grand Shrine, Jin Choukan (神長官, God Director). She is said to be a descendant of "Moreyashin" (洩矢神, the god Moreya), the first ancestor of the Moriya, according to the family tree located in the shrine. ("Moreya" is an archaic, alternate pronunciation of "Moriya".)
Sanae's sleeves are detached from her shirt, just like Reimu's. As a result, it is possible to use Sanae as the subject of the "armpit joke" rather than Reimu. However, Sanae armpit jokes are rare compared to Reimu armpit jokes.
Similar to Yukari, Sanae uses characters she's related to (Kanako and Suwako) as spell cards. However, unlike Yukari, Sanae uses characters who are her masters instead of servants.
Another palette puts Sanae in a whiteish-gray outfit, and makes Suwako and Kanako green and glowy. This palette may be a tribute to The Ghostbusters, who also wear gray and fight spirits (as Sanae now fights youkai.) The dieties further the parallel, jointly playing the part of Slimer.
In Wild and Horned Hermit, a conversation occured about an "electric rat", a thought bubble showed up with a censored Pikachu from Pokémon.