General rule, better by far to start with too many POPUP & PAUSES than to miss golden opportunities. After all you can easily tone down/turn off superfluous alerts by clicking the bottom right box within a popup. It really is a matter of personal gameplay/taste.
I also feel I want to know more of what's going on around me, for information & also immersion, & so I fully customise. Its a pain but you only need to do it once, then tweak in-game to your taste as you go.
Concentrate on setting any additional popups, & consider carefully those that you will likely want to deal with immediately (Popup & Pause), from those that will simply inform & influence any future strategy (Popup). The latter can usually wait until the next natural pause in gameplay for your consideration.
IMO Message Icons & the Log are almost useless at anything but slowest game speeds. But if you do want to actively use them, then remember to regularly review & update your "Interesting" Nations, & use the corresponding filter to avoid an information overload.