Yes your data is purged when you delete it from your activity (
https://myactivity.google.com/) (not instantly because there are many systems involved, but within a strict deadline). This is taken seriously, and there are teams at Google making sure this happens. (Not sure how much is public, but some details in this thread:
https://news.ycombinator.com/item?id=19809259) (Note that anonymized data, such as aggregate data that cannot possibly be used to identify individual users, cannot be deleted this way: e.g. (say) the number of YouTube views for "Despacito" (if you had watched it) will not decrease by 1 when you delete your activity, because that number was never associated with you in the first place.)
If something used to be in your Takeout data but is no longer there, that's most likely because Google no longer has that data about you.