Hi Jackson!
Yes, you can add items to the 'context menu' (which can be opened with a triple click on the background, or use 'Back button: show dialog' to use the back button) by adding a hotspot with the text '_hidden' in the hotspot ID, for example 'Point01_hidden'. Then it will be added to the menu but won't be visible in the panorama.
If you add these hotspots to the Pano2VR Master Node, these hotspots will be added to all panoramas. Note that the items in the menu will be sorted by hotspot title, so use numbers in the title if you want them to appear in a specific order.
Alternatively you can use '_nomenu' in the hotspot ID for hotspots that show up in the panorama but that you don't want to see in the menu.
Apparently the Knowledge Base article about this is missing, it will be added again soon.