Well, I guess you have to appreciate it in context. There are a few things to keep in mind.
A) Between the two incursions, it was highly unlikely the GTVA engaged any remotely decent hostile forces (excluding the NTF), and thus, the Hecates wouldn't have been battle-tested.
B) Leading on, IIRC, the Hecate was new around the time of FS2. This would've meant it probably wouldn't have been involved in any exercises prior to being deployed, and as such, the higher ups wouldn't have had a chance to properly evaluate the Hecate in the field and remodel their strategy around it. In particular, the protection it needed.
C) As far as the GTVA knew, the Shivans still used their FS1 era craft. Apart from a Lucifer, the Hecate probably would've been able to make short work of most Shivan vessels. Given the information the GTVA had when designing the Hecate (which was probably prior even to the NTF insurgency), it was decent IMO.
Its defensive layout on the other hand is just inexcusable. The designers had rocks in their head or placed *a lot* of faith in the fighter pilots, but you can do that when you design the ship to have a massive CAW.