Woof. Long sleep. Feeling a bit more refreshed so let's see if I understand this. As this is important for me to understand, I invite anyone who reads to comment, clarifying anything off or missed.
We are talking about an eco-system where plants and bacteria are both consuming ammonia and CO2. With the plants, the ammonia and nutrients feed the plants (there's more I know. Keeping it simple), the light provides the energy source for plants to photosynthesize and absorb nutrients (if that's in fact a word), and the CO2 provides the fuel for the plants to breakdown the nutrients absorbed from the water and substrate during photosynthesis which in turn enables them to grow.
Fish and atmospheric exchange provide the CO2, Ammonia comes principally from the fish (other sources as well organic breakdown), and nutrients come from the water and substrate.
Plants and certain bacteria compete for the ammonia and CO2 in the water. Under ideal circumstances in the tank, assuming plants are operating at peak efficiency, the plants absorb the ammonia faster than the bacteria. A balance establishes between the two where plants get what they need, and bacteria colonies grows only to a size sustainable by the amount of ammonia and CO2 available to them. (what the plants do not absorb or require). The more mature and healthy the plants, the less ammonia and CO2 is available to the bacteria, the smaller the bacterial colony. The plants have the advantage here.
Ok. Assuming all of that is reasonably correct, I'll return to the original topic, nitrogen deficiency.
As ammonia comes principally from the stocking level in the tank, the lighter the stocking, the less ammonia is available to both plants and bacteria. A limiting factor for the growth of each. As such, in the instance where the plants require more than is available given the balance of consumption between plant and bacteria, the growth could slow or stunt, which could manifest as a nitrogen deficiency in the plant.
Lighting levels will affect plants but not bacteria. If lighting levels are sufficient for the plants (assuming all else is equal) the overall energy to photosynthesize is optimal for absorption and processing ammonia, CO2 and nutrients. If lighting is insufficient, photosynthesis will slow, reducing the absorption rate of each, slowing growth. In extreme instances, the bacteria could gain the advantage in consuming and using each, stunting plant growth which could show as signs of nitrogen deficiency, perhaps CO2 deficiency as well.
CO2 levels in the water are affected by both plants and and bacterial consumption, CO2 production by stocking levels, and atmospheric exchange. Under ideal circumstance, the availability of CO2 is in a balance where plants and bacteria get the fuel they need to process nutrients; however, if, as a result of light stocking and/or too much atmospheric dissipation, CO2 is low, plant and bacterial activity growth rate slow as nutrients are processed at a slower rate. In the instance where certain plants require more CO2 than is available for processing nutrients, once again plant growth could stunt, showing in this instance a CO2 deficiency. And in this instance, fuel is insufficient, processing of ammonia could slow to the point where a nitrogen deficiency is also indicated.
Finally, nutrients other than ammonia. This is the area I will likely oversimplify the most. That being said, nutrients available keep the plant healthy, enabling the continued growth of the plant, which in turn influences the ammonia and CO2 consumption rate as well as the photosynthesis of the plant. The larger the plant gets, the more of each it will require. Insufficient nutrients will slow and I assume can potentially stop the plant's growth altogether as it will only grow to the amount of the nutrient required that is least available (I think I said that right). The deficiency for that item will show first, but in extreme cases, where the plant needs much more of that item than is available, then ammonia and CO2 could slow to the point where a nitrogen and/or CO2 deficiency could manifest.
So when trying to diagnose what is going on, knowing the plant's requirements for CO2, lighting, and particular nutrients, possible areas of CO2 over dissipation, and stocking levels in the tank. A bacterial bloom or imbalance somewhere should be considered, as should any algae imbalance that may appear in the tank.
There you have it. A bit lengthy I know, and again I invite anyone to comment for clarification or correct anything I have missed.