That's actually not quite right. His fertility/heat problems started more than 10 years prior to the end of Pendulum and that extra with them. He is back to having normal heat cycles, but they use drugs to have sex more frequently. But they both realize that he hasn't had a normal heat cycle recently and they'd been relying on the drugs. That makes them realize he's pregnant.
Pendulum came first. So honestly, ignore what's been only recently revealed in Remnant about Daath's fertility issues.
They realized Daath was pregnant because they'd always had to use the heat drugs to have sex instead of using his actual heat. They then realized it had been awhile since his last heat.
Basically, if omegas were regular women, it's the same as realizing a period is late/skipped.
In chapter 5, Daato is pregnant? So that's why Juda say all that? I don't understand...