In other words, it isn't just that she's apparently not as smart as she was prior to the reboot, but also that she's inconsistent in her intellect.
I don't think Levitz had a clear plan of what he wanted to do with her and Hunts in that respect. I think that he wanted to make Helena the brains, (witness PG uncharacteristically deferring to her in an attempt to find a plan to defeat Hakkou), and took the lazy way out by trying to make Kara dumb in comparison. Then he realized he couldn't have the super-smart alien who could handle tech well if he wanted Kara to be dumber than Helena.
Compare that to how Superman and Batman are portrayed, or were portrayed together in their series. Superman knew science and tech, and was far from stupid. he could come up with his own plans to beat the bad guys. It was simply that Batman was THE master tactician and strategist, and Superman would defer at times to that.
It would have been better if Kara had been like that, with Helena playing Batman to her Superman in that respect.