Some tech trees offer 'upgrades' that serve the same function and are an improvement in every way to their predecessor -- a strictly dominant strategy, and therefore it's not a choice, it's a no-brainer.
No, not really. For example, miniaturized weapons that perform as well as the respective older models but use less spaces, crew, energy etc. are strictly better, but they are dominant only if they are the only weapon type in the game.
Ordinarily, rock-paper-scissors structures are perpetuated with better rock, better paper and better scissors.
Upgrades often provide a tradeoff between quality and quantity (do you want to win battles with more casualties or with more expensive ones?) and a reason to invest enough on technology to keep pace with enemy developments that could make player assets suddenly obsolete (e.g. you'd better invent Teleporting Nukes before the enemy improves Point Defense Lasers enough to make short work of your stealthiest Nuclear Missiles).