In com.ibm.domino.domsql.sqlite.driver.meta.DatabaseDefinition, the immutable field MAX_COLUMNNAMELENGTH is set to 16.
It took me a while to track down why my column names were truncated.
If there's no specific reason to have this limit, I hope you would consider removal of this restriction in future releases. The headroom for the select query is quite large.
The maximum number of bytes in the text of an SQL statement is limited to SQLITE_MAX_SQL_LENGTH which defaults to 1000000. You can redefine this limit to be as large as the smaller of SQLITE_MAX_LENGTH and 1073741824.
http://www.sqlite.org/limits.html
(I have no idea how to create my own build/plugin from the source code)