Hello @alkos - thanks for your interest in SQLCipher! It is technically possible to build System.Data.SQLite with SQLCipher, however, it can be quite technically challenging. Therefore it is not a scenario we provide assistance with under community edition support due to the complexity involved.
That said, if you’d like to safe some time and use a supported solution, we do sell a pre-build ADO.NET provider under our Commercial Edition platform. Please feel free to take a look at SQLCipher for Windows ADO.NET if you are interested.