hidden object on master page

Do you work with Layers? Do that, make the stacking order of the layers so, that the objects which always have to be behind others (like background image or color) are on the bottom layer, and things which should always be visible on the top layer like page number, running headers and between own layer for images, gaphics and text.

You can Cmd/Ctrl click (with the black Selection tool) down through objects that are covering other objects in order to select them.

Master page items appear below document page items that exist on the same layer. 

You can may a new layer on your master page, move it to the top of the layer stack, and then put your items that need to be on top onto the new layer.