I meant to write this back after v5.17 expanded Notifications. Currently, the notifications page displays a maximum of 25 items, with anything older purged, and I'm unclear if this means infrequent/high-traffic users may be missing correspondence—I finally filled the list a couple days ago and while a manual comb doesn't look like anything's fallen through the cracks, an ounce of prevention stays a pound of cure.
A partial alleviation for sheer volume is user-end enabling/disabling of notifications for uploads, which are the only things not covered in user settings. (Separate tracks for Friends v. Followers is a corollary consideration.) I'm also wondering if there's an easy patch for double-notifications when a user is responding directly to another user's post: one message is for the reply itself, while the automatic @ prefix in the reply triggers a separate, effectively redundant message.
In the long term, a larger and/or more permanent log may be prudent: with S7 picking up a fresh userbase and several legacy members returning after literal yearslong sabbatical, it will drastically reduce the risk of info gaps. If server overhead is a concern, the log can automatically prune after a set interval (either for read notes or otherwise)—on dA, notifications are deleted after a year if not specifically flagged for retention.
Lastly, notifications for new forum posts parse the thread and post ID, but not any pages past the first: this means the note leads to the opening post and the user has to manually navigate to where the conversation picks up. Since "Latest Active Threads" does parse the page, presumably there's a viable preexisting logic that can be added to the notification protocol.