It has been asked for before, but there's no way I've ever seen to hide cloaked files from the Files window, I think, for a good reason...
If a file isn't meant to be in a site, uploaded, or worked with (which is what cloak and hide would mean to a developer), it should probably just be taken out of the local site all together.
Cloaking itself is meant to allow you to visualize those support files in your site window that don't need to be uploaded. Items like .DWT Template files, for example. Cloaking, then hiding them from view, could easily lead to confusion later (where did that file go) after the developer has forgotten about the hypothetical "Hide Cloaked Files" setting a year down the road.
If you like, you can make a feature request for the ability to hide cloaked files here:
Adobe Dreamweaver: Ideas: Hot (1669 ideas) – Adobe Dreamweaver CC: Feature Ideas
and/or here...
Dreamweaver support forum - Ideas
...if enough other users feel the same way and add their votes to your idea, Adobe may see fit to add the function to the program.
(I agree with Jon's assessment... If it isn't intended to be managed or transferred by Dreamweaver, it really shouldn't be in the site folder. Dreamweaver shouldn't be expected to execute OS-level management, and that would be potentially problematic were it introduced into features. I could only imagine how many countless unintended document "hidings" would cause unending file and GIT/repository errors, not to mention misleading team devs. You would be safer setting expectations and standards/convention at your team level to get your file managers to safely move the files out of the site as part of their process.)