With Xcode 8 / iOS 10 it's possible to link against both Apple's sqlite library and SQLCipher and won't warn about duplicate symbols. I experienced an issue with this scenario here, where Apple's library was used for sqlite3_open but SQLCipher was used for sqlite3_key: https://github.com/sqlcipher/sqlcipher/issues/179
With Xcode 8 / iOS 10 it's possible to link against both Apple's sqlite library and SQLCipher and won't warn about duplicate symbols. I experienced an issue with this scenario here, where Apple's library was used for sqlite3_open but SQLCipher was used for sqlite3_key: https://github.com/sqlcipher/sqlcipher/issues/179
YapDatabase/SQLCipher was unaffected but regardless they recommend adding a snippet to double check that the database is actually using SQLCipher. https://discuss.zetetic.net/t/important-advisory-sqlcipher-with-xcode-8-and-ios-10/1688