Boy, I keep coming up with gems of questions...

I really like to keep my aquariums clean. Like 100% WCs, in two sessions per week. Perhaps this is a reaction to when I didn't do them enough. Anyway, psychology aside, I really like my tanks clean, but I'm wondering if a tank can be too clean for good plant growth. As in, such low nitrate levels that the plants can't effectively use them and grow. Here's what I wanna do:

55 gallon tank, 48" long
Mix of ecocomplete and floramax substrate, with a small bit of smooth pebbles
Plants including rotala, swords, crypts, water sprite, and lilies
High light, 10,000K (yeah, not perfect but it's what I have)
DIY CO2 for now
Dosing with flourish comp weekly; root tabs near heavy feeders (lilies and swords)

Right now the tank has all those characteristics but it has small smooth pebbles as substrate and no CO2 yet. My nitrates have been below 5(!) in this tank, and I'm worried that's not high enough. Will this level naturally rise a bit since I won't be vaccuming the eco complete in the same way as I do the gravel?

Thanks for you advice. Perhaps I am overthinking this. Happy overthinking, but still crazy.