There are plenty of reasons why you could want an inferior design. I get the impression that after the loss of Earth and its industrial capacity, the GTVA lost acess to a lot of special raw materials, industrial capacity, etc. and started producing lower-quality clones of its old weapons and equipment. The Prometheus R is the most obvious example of this. If you look at the FS2 weapon stats, you'll see that they're just the FS1 stats toned down a bit. The only new weapon, really, is the Maxim, and maybe the Trebuchet since it's such an improvement over the Phoenix.
So the Hecate may be larger than the Orion, but maybe it uses less miniturization (I know), less crew, less logistics footprint, or whatever. Or, the Hecate actually has decent AAAf/Flak defenses and the Orion doesn't. Think of your own excuse.