I think you understand it now. The bookmarks are just a reminder. You can delete them if you want. Any location you've ever received a bookmark for or that you've discovered or otherwise has become known will be recorded in the galaxy-map.
There's no real hard-limit on bookmarks. When the panel is full you can page through it with the mouse-wheel.
Having bookmarks just appear when your on the planet they refer to is not handy because your destinations are often in completely other systems and that's often when you want to use a bookmark. (Say somebody gives you a bookmark to a weapon-dealer that's in another system) and you want to go there: If it only showed bookmarks of the current planet that bookmark wouldn't show.