Well cybran frigates certainly are the strongest, but the situation you seem to be describing as most problematic is before t2 navy can really get involved. However, aren't torp bombers a very good counter to even cybran frigates? I just tried testing it and 10 torps killed 10 cybran frigates with only 1 torp dying. Yes, torps cost significantly more in energy and a bit more build time, but they definitely can still be a very efficient counter. This also involved some micro though: shift g on groups of 3 to kill frigates as quickly as possible while also limiting overkill, which would be unrealistic and far less efficient if you are facing huge numbers of frigates. For example, right before that I tested sending 50 torps into 100 frigs and killed 15 frigs on the first pass, but if set to patrol after the first shift g attack, they just derp around and barely kill any additional frigs and all torps die with a large number of frigs still left. So you definitely need to micro the torps for them to be efficient. And the larger the number of frigates, I think the more effective their aa is because the torps will spend a lot more time in range of the aa.
Edit: in my next test I did 50 torp bombers vs 50 frigates and microed the torps. Ended up with 45 torp bombers left after killing all the frigs. So after that I'm left feeling like all frigates are not just completely countered, but ANNIHILATED by torp bombers, which are about the same mass cost and just need a bit more energy. But if we are talking about someone who has invested into 50 frigates, I don't think the extra couple t2 pgens you'll need for the air army that completely nullifies their investment is too much, considering how you really don't need anywhere near the same number of torps to counter those frigs. .