For the first question I have no answer. It looks a bit strange.
But, for the "hidden" files, bear in mind that Windows manipulates file permissions etc completely differently from Linux. In fact, NTFS does not support Linux/Unix file attributes at all. So that hidding did not have any effect on Linux at all. If you want to hide a file in Linux you add a dot (.) as the first character of the filename, however that file is still easily accessibe, eg "ls -a". For example:
$ touch a_file
$ mv a_file .a_file
$ ls -a
. .. .a_file
Now for the Trash folder you saw, if you deleted these files from a file manager in Linux, it just moved them to a special folder called Trash, the equivalent of Windows' Recycle Bin. If you delete them from command line with rm they should be totally deleted.