This has been discussed before, raising an issue to track it.
The general idea: Some way for users to say "I want these types of notifications in-app, these ones in email"
Solving this problem will also mean we will need to consider the use case where the user has not logged in for a long period of time - should Workbox send a quick digest to say "here is what is waiting for you.."? Just something to consider
If you are going to comment on this ticket, it would be nice to hear from you which specific notifications you are thinking about only having in-app (it would help us understand what should be our sensible defaults)