Well I can't say for sure what happened for you, I wasn't there. Maybe its the point at which you grabbed it, maybe it was random luck for you (people have pointed out that the hyperdrive blueprint is in the random rotation so for some they just got it by luck of the draw), maybe it has to do with the Atlas (I said yes for what thats worth) or maybe it just doesn't happen 100% of the time. It's a flawed train of thought however to say "well this thing didn't happen to me, therefore it doesn't happen. Other people must not know what they are doing".
For me - I repaired my ship, went up to the station and immediately got the bonus ship. I messed around mining for a bit, then went to a second system. Here I spent a lot of time exploring and earning units. I saved up and bought a 2M unit ship, and didn't give it a second thought that it didn't have a hyperdrive on it. I assumed I could make one, or that it would transfer over. It didn't and I can't. I didn't get any kind of a quest pop up. I then spent around 10hrs exploring this system, found dozens of tech blueprints, but no hyperdrive (I did however find all the BPs required to make warp cells).
At this point I started questioning what the hell was going on - I'm now 15hrs in and can't leave my second system. I had no idea there was a bug, or that other people got their hyperdrives in 30-45min via a quest. I found all this out killing time at work a few hours ago, at which point I realized "Oh crap, I may be screwed here..". I have no quest, I have no blueprint, I have no hyper drive, and no ships that I can buy have one either. I'm going to be in my second solar system until they fix the quest, I randomly roll it as my drop from a factory, or I quit and restart. I'm not planning on restarting yet.