I wouldn't say Facebook apps were forgotten as much as actively suppressed by Facebook after a certain point in time.
In the early days of the platform app developers had a huge amount of freedom in terms of accessing users' social graphs, pushing notifications to timelines, and so on. It made it incredibly easy to build a viral loop and push out an app that spread like wildfire.
Obvious downsides to that - big privacy issues, and annoying users with endless notifications like you said. Facebook had to start restricting what app developers could do, and once that happened it became much harder for apps to get traction.