A business dropped deposits into the night depository. Later in the day, an employee dropped off more deposits for the same business that were locked bags through the drive-in. Deposits that were dropped off exceeded $10K in cash. Does the person dropping the bags off need to be put on the CTR under the person conducting the transaction?

The only reason you don't have to ID the person conducting a deposit via the night depository is that you can't reliably know who did it. With a "drop off," you have at least a chance of knowing who the transactor is. That person needs to be identified on your CTR.