I tried moving (with the built-in "Move To…" file action) some files from one hidden folder to another (first a bunch of files, then just a single file). Nothing happened. I tried it again, creating "~/text.txt" and trying to move it to "~/.test/". Nothing happened again. I have tried both using the file selection hotkey from Finder, and also navigating to the file from Alfred's file navigator.
I am using Alfred v2.5 (295), OS X 10.9.5.