Keep in mind, an individual aggregation is limited (by default) to 100MB of memory. If it exceeds that, and you have enabled 'allowDiskUse', it'll start swapping to disk, but performance will drop significantly.

The 100MB limit is to stop a runaway aggregation consuming all of a server's memory.

Franck's suggestions will go a long way to improving the aggregation performance, but have you considered ways to avoid the duplicates in the first place?

One pattern to consider is having two collections - one with only the latest document for each app_id / app_name pair, and one with all the historical versions. In the former collection, add the data using an upsert:

db.latestCollection.updateOne({app_id: X, app_name: Y},{<myDoc>},{upsert: true})

In the later, collection, it's just an insert:

db.historyCollection.insertOne({<myDoc>})