Unity iOS can handle SQLite even with Byte-Code Stripping on.

There are some things you need however
1)
Copy (...Unity.app/Contents/Frameworks/Mono/lib/mono/unity/Mono.Data.Sqlite.dll) to ([ProjectFolder]/Assets/Plugins/Mono.Data.Sqlite.dll) (If you want to not use the .NET subset use the folder 2.0 instead of unity

2)
Create a file in assets called 'link.xml' and inside that write:
Code:  
      
      
  1. <linker>
  2. <assembly fullname= "mscorlib">
  3. <type fullname= "System.Globalization.CultureInfo" preserve= "all"/>
  4. </assembly>
  5. </linker>

Then you can start including Mono.Data.Sqlite and run under the .NET Subset with Byte Code Stripping on. There are about 5 other required DLLs but they should manually include. If not every time you see an error about a DLL not found put it in plugins from the same Unity.app folder.

Edit: The extra DLLs that should be added implicitly from the Unity Folder: System.Data, System.Core, System.Transactions, System.Xml.

So far it's been working for us like a charm for months.