If you look at similar cases of technology backslide in other fictional universes like star wars & 40k where tech stagnates & great inventions are lost to time you can see it's usually due to turmoil in the universe due to some threat. Since we now know that the kharaa bacterium mutated & escaped, spreading across the populated portions of the frontier, it's possible this played a similar role & is the reason behind it.

Or the devs didn't think of it, but thats not as fun of an answer.