Yes, the “are you sure” is sometimes useful, if you’ve made a mistake and selected more than you meant to. But for me, it’s so rarely that it’s not worth the bother of being asked every time. I’m usually pretty aware of what I’ve selected to delete, and if I make a mistake, I’ll notice it and hit “undo”. Plus there’s the “history” function. So it’s maybe once in several hundred deletes that it might actually save me a little effort, but the rest of the time, day in and day out, it’s just annoying and wastes time.
For “tool tips”, i.e. information that pops up when you hover over something, having at least a global switch in settings to disable them is helpful. A step up is to have an option for a hotkey you can use when you want to show them. For modal alerts, the best system I know of is where there’s a checkbox saying “don’t ask again” or “don’t show this again” in notifications. Then in the settings there’s a button to reset all hidden notifications. That way people can customize the notifications they find useful or not. There could be a deluxe version where you get a list of all notifications and choose which ones you want, but that might be overkill…