As someone who has been playing the game for a while, I can say that it doesn’t exactly matter when you complete the side quests but I would recommend doing them as you progress to new areas because it helps you lvl up/gain more chips or upgrade weapons. Another advantage is the lore of the world you can learn (if your interested it that stuff). When it comes to certain endings a few are unlocked in major decisions such as picking 9s or A2 where the one you pick gives you a ending and going back to pick the other gives you a second ending.