Relax - the top ship challenge is only for level 77+. It's likely that another tier of challenges will be released (alongside hardware abilities?) that will have better drop rates (and likely ship omega mats?)
I think this was a smart play - put a challenge out there to give us a real reason to invest in ships, but keep drop rates low so those who focus on ships don't have unreal advantages at first. As ships progress, they'll probably be more impactful on the rest of the game. But for now, just be glad you are ahead of the majority of players and you now have access "free" (term used loosely) zetas and a jump start in the next tier of challenges.