Try to poke your wood with fingernail to see if it is getting softer. If it's rotting then I could see it contributing, but not really sure how much. Then again I have a piece of wood root (forest find, not an aquarium product) in my tank that was there for over 4 years. it is getting softer in few places, almost spongy in some, comparing pictures from back then to now I noticed how much thinner it became. Yet my nitrates are 5-10 ppm, I feed more then I usually did . So in my case I can't tell if the wood is contributing (still plan to taking it out soon).
Interested to find what others think.
In your situation I think I would attempt to build dedicated de-nitrator filter. Think 2-3 inch pvc pipe closed from sides, loaded with seachem de-nitrate media, through which water slowly moves. As far as I understand it the key is "very slowly"(and it takes looong time for the third type of bacteria to establish). Was thinking to use the membrane aqualifter type wet/dry pump, it kinda just drips through. I bought a bucket of media but never went ahead with the build so can't report the actual results.
PS,
To be honest I'm actually quite surprised pleasantly about my nitrate situation (hence never went ahead with denitrator). Can't tell for sure but it might be that deep sand - I have ecocomplete capped with sand about 3 inches total depth-l. Perhaps thats what doing the final nitrogen conversion in my case. I never change more then 4 buckets in my 125 and I'm quite lazy with it too so it could go for months.