The challenge runs three times per week, you get two bites at that apple, and get at least 2 Omegas per challenge (Can you get 1? I'm not logged in right now so I can't verify, but I don't recall ever getting less than 2), which means 12 per week just from the challenge. That's actually more than regular omegas per week.
The problem is that fleet omegas are still relatively new, so folks have barely had time to finish off their first ships and now that the ship meta has shifted a little they're having trouble getting the omegas for their new ships. It's kind of like when omegas first came out for characters (Remember that? Pepperidge Farms remembers.) and folks were legit arguing back and forth about how you should put an omega on Old Daka's basic or HK's leader ability first or second.
My issue isn't with omega materials (Although I'm short on them, to be clear, just like everyone else) it's reinforcement materials. There's no challenge for those, though you can get a few from an event once every couple weeks, and the first few fleet boards don't give any as drops.