Just because they reverse engineer it doesnt mean they dont know how it works
But they don't actually reverse engineer anything. They just find old Forerunner tech and use it. They don't know how it works, or why it works, they just know that it works. All they do is copy existing stuff, with out learing how it works.
Halo Array: Seven giant rings scattered through out the galaxy, a weapon of last-resort against the Flood parasite. They are 10000 kilometers in diameter. Main Weapon is a radiation pulse of unknown type with a range of 25000 light-years that kills all life large enough to support the Flood parasite along with all Flood forms above Infection Form. Status: Standby Mode after Delta Halo firing was aborted.
The Onyx Shield World: Onyx and a second Shield World in Halo Wars I do not know the name of are the only known Shield Worlds, it is made up of trillions of the advance Onyx Sentinals. The core of the planet houses a Slipspace rift which within is a Micro Dyson Sphere and a star. Onyx may be able to fire at DS or beyond levels. Please refer to the book Ghost of Onyx. Have to go now, edit this later.
The Ark: The Ark is the nerve center of the Halo Array and the largest Forerunner refuge outside of a Shield World. It can remote actiavte the entire Halo Array if the firing of one is stopped. It can also build new Halos within a few months using the resources of a large planet located at it's core. The Ark was either badly damaged or destroyed when the new ring destroyed it's self will firing. I will do another post about Covenant ships based off Halopedia data.
But none of those actually help the Covenant war effort, plus none of them are Covenant, either. The Halos wipe out all sentient life, so if they used them, the Covenant loose, along with everyone else. Plus, they are pretty much immobile, and as they are all located in a different galaxy than the Empire, firing them would just kill the the Covenant + UNSC, no one else.
The sheild worlds, as far as I know, cannot be controled by the Covenant, so are just as likely to attack them as it is the Empire.
The Ark, again is immoblile, and its only purpose is to create more Halos, which, as I said earlier, are a no-win for everyone.
The Empire, on the other hand, has superweapons that they can control themselves, are mobile, and won't they won't kill themselves if they're used: The Death Stars, Sun Crusher, Galaxy Gun, Eclipse I+II, World Devastators, etc. Granted, most of those weren't active at the same time frames, but they are still worth pointing out. Plus there is the regular Super Star Destroyers, and the massive fleet that is many, many times larger than the Covenant's.