@rajendradewani - If you are providing a key (e.g. via sqlite3_key or PRAGMA key), then SQLCipher encryption will be active. If you have not provided a key after opening the database, then it will not. With respect to performance, I would suggest taking a look at this post on SQLCipher performance, which explains so of the practical impacts of SQLCipher and how to ensure optimal performance.
With respect to temporary storage, those are different than in memory databases. You can look at the “Database Encryption and Temporary files” section of the design documentation for more information about what is / is not encrypted.