I see delays in notification emails sometimes in the order of hours. It doesn't always happen.
Has anyone else been seeing this? Why do these happen? Is there any way to address these?
There are no known issues currently with the Notifications that can be set from the 'My Settings' -> 'Notification Rules' page.
There are known issues with Watch emails sometimes being delayed. Watches are set on specific work items.
If you let us know for sure to which one you are referring, we can open a Support Case to add you to the existing Defect for Watches or investigate further if it is for Notifications.
This happened with a couple notifications (and not Watches).
I'll open a support ticket for this then.