Fast construction vastly improves the performance of your empire, as you can get more ships built in less time. This allows overwhelming of enemies (or keeping up if they have the same construction rates), replacing lost forces quickly, etc. Why do you think the Space Yard technology is so expensive?
Also, if you go with Monoliths (for a vastly superior economy in the long run), you can get them built in 3 turns at planets with a Space Yard II and 1 M population with just a 34 percent bonus to SY rates, whereas you can never get them built in less than 4 turns with no bonus in SY rates without lots of population (2 billion in fact) on the planet. A 12 percent bonus will let you build them in 3 turns with Space Yard III, but those are much more expensive to research. Please tell me how that does not improve the performance of your empire?
Furthermore, higher SY rates help you get stellar manipulation ships built a lot faster, which is definitely a big plus. Say the ship costs 100k minerals. You are building at a planet with 1 M pop and a SY III (for simplicity of calculations). That will take you 34 turns with no SY bonus (100k/3k). But with that 45% bonus to SY rates, you can build it in 23 turns (100k/4350).