Why is my hard disk not put into sleep mode if the application is running?

If one or more hard disks are equipped with temperature sensors, the values will be read out in regular intervals. macOS is interpreting this as access to the hard disk which causes the disk not to be put into sleep mode.

You can change this behavior by enabling the disk saver feature of the application: When you are inactive and the computer is not really in use for some period of time, the program can automatically stop all sensor communication with your hard drive(s). This allows the standard sleep feature of the hard drives to become active. Just open the preferences window, go to the General pane and set the pop-up menu of the option Disk Saver to the desired time-interval for user inactivity.

Further information: Setting General Preferences