Yes, well, remember, The Helghast were powerful, they ahd a very large Fleet that was waiting in their home system to attack, but the Inquisition pushed them back in this case. The helghast had broought out EVERTHING do protect the ZKW device, but they failed.
And the Inquisition uses fighters for its members when they are out in the feild doing their regular work, but Inquisitor Lords can use Cruisers. Hence the Defiant. And in the terms of the Battleships? Those are kept in reserve for the big fights.