The Reason browser only displays file types that are relevant for the device that currently has Browse Focus (orange frame and orange header in the browser).
If a ReFill or folder in the browser seems empty, it could be that the folder doesn't contain the file type you're currently browsing for (for example, looking in a folder of samples when browsing for patches or vice versa). Also, the browser will always hide empty folders.
If a ReFill or folder contains files that don't have any compatible device type in Reason 13, these folders will appear empty. This could, for example, be if you are browsing for patches for a Rack Extension or VST that isn't installed on your computer.
To see all the content in a folder, open the browser without Browse Focus, e.g. by pressing [F9] (so that the browser opens with a grey header). Note, though, that the browser only shows file types that are relevant to Reason, e.g. patches, samples, MIDI files, REX files etc.
Another thing to look out for is that some folders are blacklisted by Reason 13, i.e. the Reason browser won't look in those folders:
Blacklisted folders on Mac:
The following folders are disregarded by Reason 13 on Mac, so make sure you don't store any Reason related content/files in these:
Macintosh HD/Applications
Macintosh HD/Library
Macintosh HD/System
~/Music/Propellerhead Content/ (in your personal Music folder, where the old Optional Rack Extensions and ReFills in Reason 12 were located)
Note!
Even though "Macintosh HD/Library" is blacklisted, "Macintosh HD/Library/Audio" is explicitly whitelisted, so you can create shortcuts from there.
Blacklisted folders on Windows:
The following folders are disregarded by Reason 13 on Windows, so make sure you don't store any Reason related content/files in these:
C:\Windows
C:\Users\<youruser>\Music\Propellerhead Content (in your personal Music folder, where the old Optional Rack Extensions and ReFills in Reason 12 were located)