I understand your issue. Files Gallery is of course a file browser, and will simply display everything in the folders, just like any other file browser, including desktop browsers. How you choose to use it is up to you of course, and Files Gallery won't care about storage space or inode availability.
As for displaying a thumbnail for zip files, this isn't something any other file browser does. If it was to be done automatically, it would require opening the zip files (on server via PHP), and extracting images inside (if there are images inside). If the zip file is 1GB, this could of course be a very demanding process, and could easily timeout. Besides, what kinda icon/thumbnail combo are you expecting here? A zip icon with a small image overlay?
What I can probably offer soon, which would apply to ALL file types, would be the option to host a custom thumbnail for any file. For example
myfile.pdf could have a thumbnail file
myfile.zip could have a thumbnail file
_files_myfile.zip.jpg. This would load the entire image, just as if the file was an image ... It wouldn't display the image over another icon that represents the file type (this would be obscured by the image anyway).
As a workaround, why not just display a preview image beside the zip file? Or even hide the zip files, and then force the "click" to open new window targeting the zip file it represents.
To me, this doesn't seem like something a File Gallery should be solving. If someone asked me to "create a website where users can click an image to download a zip file", then I would just create that manually. It's not really a file browser is it?