I am not a battery expert, but following lists my understanding.
1. Battery cycling affects the battery life most, but it depends. One full cycle is from fully charged to near depletion and back up again. Tough on battery. But if you keep topping it up, say, whenever it reaches 80%, you are using the top 20% of the capacity and 5 times the charge (5X20%) is counted one full cycle.
2. Lithium battery prefers to be topped up all the time, although it retains the charge longer than any other battery type. My SE is a little over a year old, but the way I use (2nd line, and always topped up), it has not lost the initial performance.
3. Yes, new OS updates might affect significantly on the battery performance (in theory).
4. You may already know, but the following link (battery university) might be an interesting read. This article is fairly old but I do not think its content is obsolete.
Basic to Advanced Battery Information from Battery University
5. CoconutBattery app is supposed to give you a number of cycles the battery went through. I use other battery app but it only shows how much capacity the battery lost over time.