Disk usage is not displayed correctly on winbox, web and SNMP. Tested on in 6.42.7, 6.44.5, 6.44.6,6.46.2 on device LHG60, WAP60x3.
On devices with 16MB storage, the usual file storage you see in file list is not non-volatile, but rather RAM disk. So if you reboot your wAP, you loose files listed on your first sreenshot (OK, in this particular case it’ll try to upgrade ROS version and then remove the npk). But if you had some exported configuration files or scripts in file storage (in root), they would be just wiped upon reboot.
The real contents of non-volatile storage is under /flash. Built-in flash, however, is used for installed system which is not shown in your screenshots. On my 16MB device, file list is empty, and still displays 988KiB free (out of 15,3MB total space).