Cost. I think all of the 5th generation were top loaders. On the cd audio side nice stackable separates were tray or slot. Cheap stand-alones were top.
6th was a split but then I think the perception of slot or tray loading being more prestigious moved everyone to slot/tray.
Plus I think top loaders might have been less secure. I certainly remember a number of physical mods or swap techniques that defeated top loader security very easily.
Same thing happened with videos as well. Started with manual top loaders and then moved to slot.