Yes.
Shinto shrines were erected during the Japanese colonial era, and near the end of the period, each village had their own Shinto shrine. However, afterwards they were torn down. The main shrine, the Chosen Shrine was removed in October of 1945.
The Chosen Shrine was built on Namsan (Mt. Nam), one of the four guardian peaks of old Seoul (Namsan, Naksan, Inwangsan, and Bukaksan). Unlike the colonial Governor General building, built in the courtyard of the palace, the shrine served no purpose other than as a place to worship the Japanese emperor^*, so it was one of the first things to go.
I linked a whole blog of photos of the Chosen Shrine, but it's all in Korean. You can see from the photos the location in the city. The second photo in particular shows three labels - Namdaemun, Chosen Shrine, and Seoul Station. Here is a Google Map from today to give you an idea of how prominent the shrine was. These days, the area is part of Namsan Park.
As far as the local shrines, they would not have been anywhere near as large or ornate as the Chosen Shrine - a simple pagoda in a village square or a local park. As the purpose was gone, there was no reason to maintain the shrines. Further, if any Korean wanted to continue the practice of Shinto, they would have been labeled as a collaborator and, at a minimum, shunned by the community.
