Layers are global, so if you turn them off one place, they are turned off everywhere.
Also, the layers panel has changed radically starting in CS5, so you now actually can see what is on each layer, a la Illustrator, and show/hide individual objects (which are not global -- they live onthe layer on a particular page, which might or might not be the master).
Fastest way to find something is to open a page where it shows and try to select it, then look in the layers panel. If you can't select it, either it's locked (also visible in the layers panel, or it's on a master page).
Is there any way to identify which layer is which, or to view the properties/contents of each individual layer (specifically these blank boxes on the Master page)? OR is there a better solution?
Which layer is which? Well, if you are in View -> Screen Mode Normal and have turned on View -> Extras -> Show Frame Edges, then every frame on the page has a color, and the color is defined in the Layer Properties. (Screenshot didn't catch my mouse pointer, I had to draw it in...)
Often when printing companies have a template for people to download it is usually not an InDesign template file.
Is is often a graphic; an EPS, PDF,Tif, or Jpg that can be placed on a layer to make sure elements are placed correctly.
Since this is probably one of these, try looking in the Links Manager for something with an unusual name that might be the template.
The Links Manager can tell you on which page it resides.
If you select the linked file in the list and click the page # to the right or the Go to Link icon at the bottom (Page icon with an arrow) it will go directly to the page and the item will be selected.
We don't know how it was originally placed, it might not even be on a Master Page. It might have been placed on Document pages, maybe even more than once.
Once you have determined where it is, the quickest way to hide this is to create a completely new layer and call it something like "Template - HIDE THIS!"
Drag the selected template image (and only the template image) to the new layer in the layers panel. As Joel Cherney has show above. the highlighted item on the page will have a colored dot to the right in the layer.
Drag this dot to the Template layer and the linked item will be moved there. You can then hide or delete the template layer.
It is also a good idea to LOCK any template layer since locking it will prevent you from accidently placing or moving elements onto this template layer!