If you really want to use the hibernate property prefix it with spring.jpa.properties. as those are added as is as properties to the EntityManagerFactory. See here in the Spring Boot reference guide.
spring.jpa.properties.hibernate.hbm2ddl.import_files=file1.sql,file2.sql
However you can also use the spring.datasource.data and spring.datasource.schema properties to your advantage. They default to respectively data and schema. As you can see in the DataSourceInitializer class. You can also set them and they take a comma separated list of resources.
spring.datasource.data=classpath:/data-domain.sql,file:/c:/sql/data-reference.sql,data-complex.sql
It gets even better because the resource loading also allows loading resources with ant-style patterns.
spring.datasource.data=/META-INF/sql/init-*.sql
spring.datasource.schema=/META-INF/sql/schema-*.sql