It depends on what you mean by hidden like no desktop shortcuts? Those are easy to remove. Many programs see the do not create startup group where nothing is seen in the Start>Programs group.
If you have a program without a desktop shortcut you can browse with Windows Explorer and drag a shortcut of the executable onto the Start>Programs menu to see it added there. You simply drag that into a folder in the Programs menu like seen in the image here for the System Info for Windows tool.