Hi,
I wanna hide a slide and therefore won't be shown in contents popup. It has a master other than other slides' master.

AFIK the list is generated at runtime so is a live list of content. There isn't a built in flag to exclude pages.
I'd be tempted to add a button on the masterpage linked to a pop up.
The pop up would be populated with the page list and the items have a navigation action attached to them. You get full control over what appears and what doesn't.