DBD::SQLite basically gets compiled from the SQLite source code, together with some Perl-specific C code ("XS code"). Simply replacing the SQLite.dll with a DLL that was not compiled from the XS code in DBD::SQLite will not work. You will have to recompile DBD::SQLite with the sqlcipher source code and then also think hard about the new API to pass the decryption key around.

Recompiling DBD::SQLite with the sqlcipher code should be fairly easy:

1. Download the sqlcipher package
2. Download and change into the DBD::SQLite package directory:

   > cpan
   cpan[1]> look DBD::SQLite
   [download]

3. Replace the sqlite3.c and sqlite3.h files with the files from sqlcipher
4. Use the standard invocation to compile and install the module:

   perl Makefile.PL
   dmake
   dmake test
   dmake install
   [download]