The biggest weakness is the cost. Each client would have to purchase an expensive license. The source code is provided upon purchase though, but essentially destroys the ability to build a client from source due to the compiled binary distribution.
I really doubt it. I have not seen any evidence to suggest that there are irreconcilable issues with SQLCipher's page level encryption over a flat file. Codebook, Enpass, Signal, and a ton of other important clients use it just fine.