Is it possible to hide files from Terminal's ls?
Hidden files are hidden from ls unless you use the -a or -A flag:

-A   List all entries except for . and ...  Always set for the super-user.
-a   Include directory entries whose names begin with a dot (.).


Source: ls man page

Therefore, files can be hidden by starting the filename with a . but ls will still show the file if it is run with -a or -A.

Note that not all files that are hidden with a . are malware-related. The system creates many files like this for a variety of reasons in various places on the disk that can cause problems if removed or modified.