When looking and skills and effects that are not gained by skill gems, but some other way, is there a good rule of thumb to know if these are affected by our passives/items/flasks/ascendancies?
Yes, but it’s not going to come in the form of some big list of things that work with other things. It comes from understanding the mechanics, which determine all the results. In general, any of your modifier stats apply to anything you do (that is the thing they apply to).