If the "ceramic" refers to the ceramic disks that go in the first basket of Eheim (and Rena and Fluval) canister filters--they are completely inert and will not affect water chemistry. Their sole purpose is to remove large debris so it doesn't clog the finer filtration further along.
The numbers you post indicate a real problem in the aquarium which I'll try to help you figure out. First, nitrates at 50ppm means insufficient water is being changed regularly. The lack of live plants means there is nothing to use the ammonia/ammonium so bacteria convert it to nitrite then to nitrate--and there it stays. Until you remove the water. In a plantless tank, a weekly (every week) water change of 50-70% is advisable. I do 50% weekly and I have heavily planted tanks.
While many will argue that nitrates are "harmless," the fact is just the opposite. Many fish are adversely affected by nitrates at this level, some even lower. Nitrates at 40ppm is generally considered the highest, and preferably they should never be above 20ppm. In planted tanks they are often below 5ppm and frequently zero. But that's the plants working for you.
Second thing that pops out is the increase in hardness. If the tap water is 6 dGH, the tank should not be 9 dGH unless due to something calcareous is in the tank. And if that were the case, the pH would also rise correspondingly. A pH of 9 out of the tap and 5 in the aquarium is almost unheard of. Are you certain of the hardness readings? Can you contact your water supply people to ascertain their hardness measurement to compare? This frankly does not seem possible.
The petrified wood--do you actually mean "petrified?" This is a rock. Real wood will partially lower the pH, but not to the extent you describe.
Soft acidic water fish would have a perfect home in this tank, once the nitrates are lowered of course. It is only livebearers that will not manage.