Intergalactic Summit

It is clearly that you problem is not microbiological or organic in nature, since you already tried ammonia and acid based products. Are you sure that the smell is coming from you cargohold and not another part of your ship? Do you have the habbit to collect Frozen Corpses after pvp engagements ? It could be that your refrigerating installation is not working properly and they have began to seriously decompose and therefore causing leeks into you cargohold…

If this is not the case, your problem needs a more in depth approach on atomic level. You have flown you ship close to the sun with the cargobay door opened , it’s clearly that you have forgotten to deactivate shields so that the radiations may get in. Proof is that your ship survived your little experiment. No need to take the trip once again tho ;)
You can easily generate a source of radiation - while docked - in your cargohold . There are 2 approaches to this:

1) The classical Enriched Uranium core, but make sure that the Sterile Conduits in the core have a filter consisting of Hypersynaptic Fibers impregnated with Powdered C-540 Graphite as moderator. Needed quantities of Heavy Water goes without saying. The downside of this is the nuclear waste formed after, which mainly consists of Caesium and some traces of Strontium Clathrates .
Caution ! The ship’s cargohold and Reactor Control Unit must be shielded by diverting power from the weapons or shields to prevent any unwanted interference. I strongly suggest that you also equip your Omen with a Damage Control Unit ( God forbids for something to go wrong, otherwise you risk lifetime enslavement as a hard labor to pay for the damage costs done to the station owner where your ship is docked) ;

2) Thulium Hafnite . That because thulium is not particulary toxic to biological organisms as a metal and it’s also an excellent source of X-ray radiation. Hint: It decays in erbium and ytterbium , so make sure you purchase a detector.

If none of the above mentioned methods don’t give up any results, I strongly suggest you to contact Dr Caymus asap !

P.S. Don’t reprocess the ship, it’s such a fine vessel to have  !