Downloads folder is showing empty when it's not!
The ls manual page explains this:

total 16


Total, here, does not represent the number of items, but the sum of the number of BLOCKS allocated to the files in the directory. 

For example, if the block size is 512 bytes (don't quote me on this, but the math checks out), and the total disk space used by the directory is 8KB on disk: 

8 KB = 8000 bytes 
8000 B/512 B = 15.625 
Rounding this value up equates to 16 blocks. 


My empty Downloads directory reads the same:

njboot$ ls -axhl ~/downloads
total 16
drwx------   4 njboot  staff   136B May 16 20:17 .
drwxr-xr-x  20 njboot  staff   680B May  9 10:02 ..
-rw-r--r--@  1 njboot  staff   6.0K May 16 20:17 .DS_Store
-rw-------   1 njboot  staff     0B Dec  8 14:27 .localized