edit: many thanks for all the answers. Here are the results after applying the optimisations so far:
As mentioned elsewhere, lose the indexes on the boolean columns, they will almost certainly be slower (if used at all) than a table scan and are going to use space needlessly.
I'd consider applying a simple compression to the words, Huffman coding is pretty good for this sort of thing. Also, I'd look at the signatures: sort the columns in letter frequency order and don't bother storing trailing zeroes, which can be implied. I guess you could Huffman-encode those, too.
Always assuming your encoded strings don't upset SQLite, of course.