Note, this isn't just about the WHERE clause. You can also potentially eliminate complete hits (joins) on tables if you don't actually need to filter on them based on input parameters.
I am wondering - why are you looking to get rid of a java process that already creates the proper (assuming it does) dynamic SQL?
Best,
Kevin G. Boles
SQL Server Consultant
SQL MVP 2007-2012
TheSQLGuru on googles mail service