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In the Organize (sic) menu, select Folder and Search Options, View, and then enable "Show hidden files, folders and drives".
What folders are you actually looking for? Don't think there are any more folders than those unless you create them, hidden or not. There are hidden files in the Android_secure folder which you should be able to see through Windows explorer.
That said, shouldn't you actually be creating folders for your use? Since you are already connected through the PC, and the phone acts like a thumbdrive, just treat it as such. Right click and choose add folder... etc.
Not sure if that's what you want.
When I look at /sdcard in My Files on the phone, I can see more than 30 folders for different apps etc.
That's the internal storage volume; external cards are mounted as /sdcard/external_sd.
With the handset connected to the PC via USB, you should have two removable drives visible in Explorer. The first will be the internal volume, the second the external card.