The ought system -- 3/0, 6/0, 8/0 etc. -- is a marketing thing and varies from manufacturer to manufacturer (kinda like hook sizes.) 6/0 from one manufacturer will be thinner than the same manufacturer's 3/0 but might be the same as an 8/0 from another manufacturer.

Denier is a textile industry standard. It's the weight, in grams, of 9000 meters of thread. (Just looked it up. Ain't the internet great?) So, one manufacturer's 90d thread should be exactly the same size as another's. Most tying thread manufacturers are listing denier on their products now. I would imagine that the denier is determined before any coatings, like wax, are added to the thread.