I've used SQLite with a 5GB database and tables up to about 15m rows, and while I've certainly managed to chew up a lot of disk (same as SQL Server or Postgres), it's not the day to day experience, even with quite complex queries. All you can do is EXPLAIN QUERY PLAN, or perhaps look into putting temp files in RAM, if that is more plentiful:

http://stackoverflow.com/a/19259699/24618