nigle,
I agree in part with what your saying, but let's take another common substance, ammonia...
There *IS* always *SOME* ammonia in your tank, even after the cycle, because the fish are constantly putting in there, but your biological filter is consuming it, and when you test the water, your test kit will read "0", because it's just not possible to measure what small ammount of ammonia is really in that test tube with the tests we use.
Likewise with nitrate, I agree that extreme nitrate levels generally don't cause major problems, like a high ammount of ammonia or nitrIte would. However, since it's possible to establish a biological filter for nitrate (poor oxegen enviroment bacteria) to consume it, why wouldn't we want to?
I've noticed that even with my levels at 20-80 some of my corals have "browned" (due to the increase in thier symboitic algea).
I know the pure-ists here are going to hate me

/ but I've ordered some AZ-NO3 (absolute zero nitrate). The product says that it binds to nitrate in the water, and helps your skimmer to pull it out. I figure since my bacterial filter for nitrate isn't quite there just yet, I'm going to help them out a bit by removal of the high load of nitrate (very similar to doing a water change in a cycling tank to lower the ammonia levels back to "safe" to continue the cycle).
In fact, I'm looking at this product in the exact same concept of cycling a new tank, though at this point the ammonia and nitrite filters are established and handling the load, the nitrate reducers are not yet keeping up with the production, so I'm going to help them out. The idea is to "ween" the tank off the nitrate reducing product until it can handle the load itself without the additon of any chemical product.
So getting back to the original topic "long term effects of nitrate", I belive strongly that high nitrate levels encourage algea growth (even the "good" algea living inside our corals, clams, etc.) and because of the excess ammount of algea in the tissues of the corals will cause them to "brown out". I can't remember where I read this, but one author belived that if high nitrate levels were left unchecked (ie way more that 100) and the algea in the tissues of the corals were to keep reproducing, that this will lead to the expulsion of the algea from the coral (bleaching).
Anyway, it's time for me to run another nitrate test tonight, I guess we'll see if Seachem's De*Nitrate product is still working....