I'm transitioning an application from using a normal SQLite database to one with full text search enabled. It has several BLOB columns that store things like digital signatures, which obviously do not need to be indexed. I've read that other people solve this by moving all non-TEXT data to a separate, non-FTS3 table that they inner join with the FTS3 table when necessary, but this is a very inelegant solution. Is there no way to simply exclude certain columns from indexing?
It's not inelegant. SQL is relational, joins are a natural part of life. Thinking they're "inelegant" is what leads to stereotypically poor database designs.
You've determined you have two different kinds of data -- text you often need to search, and blobs you do not. There is absolutely nothing wrong or inelegant about storing these in two different tables.