@tcoyle I was able to build a reference project using a similar configuration (i.e. SQLCipher via CocoaPods, using Xcode 9 beta, targeting iOS 11 and the 5th generation iPad). There were no build errors, and everything worked smoothly.
Based on our past discussions, I recall that your project is much more complicated, with multiple pod dependencies, configurations, schemes, etc. In this case from your build output, we can see the -DSQLITE_HAS_CODEC, but it is theoretically possible that a sqlite3.h file is being picked up from some other include directory, of which there are numerous.
In order to narrow this down, I would consider adding a header search path explicitly referencing the location of the SQLCipher header above everything else, or adding the .h to your project explicitly, so it is first in line. If that resolves the problem, then it would be helpful to search the other include directories to see if there is a conflicting sqlite3.h present.
A project configuration like this could have been present earlier, but manifested only as a warning whereas now
[-Werror,-Wimplicit-function-declaration] is treating it as an error.