Have you noticed when you minimize the icon size to the smallest on HOME Menu, the maximum allotted slot is 360? Maybe that ties in with the badge limit if you try maxing 3DS and DSi titles. I think there's a GUI rendering issue in there, too if we want to break it.
I've never counted all the slots, I've always kept all my games in folders using up minimal space on the overall main menu, but what you say doesn't surprise me. The Wii U behaves kinda similarly, if you fill up all the pages or close to all the pages with games, more pages will appear on the Wii U. The amount of allotted space has never been the issue for either system especially considering we can create folders to store more things in, 300 is just some programmed limit pertaining to the 3DS titles specifically that the badges seem to be tied to as well. And as we know, we can install well beyond 300 titles, and they're all actually there on the 3DS, we can access and launch them through various HB apps that can launch games, but the programmed limit just pertains to what actually shows up on the main menu. One would think that theoretically this could be changed for CFW, but I understand, far easier said than done.