You really has no reason to add NetherOres other than the fancy PigZombie anger and random explosions on Ore Mining into the Nether.
As for CoG and Harvestcraft, I don't know these mods. Though if they properly reference the Ore Dictionary in recipes, you may totally replace these mods Ore Generation by GregTech. If not, you still can go set proper unification targets in GregTech.
A better choice is let GregTech generate its ores in nether as its standard settings.
If you need other kind of ores not generated by GregTech or some mode require more amount of some specific ores, then you may configure some Custom Ores or adjust settings for existing ores into GregTech worldgen.
GregTech is a very complete and challenging mod with clever; long thought, refined and probably math driven settings.
There are few mods that can coexist as is, without disrupting GregTech equilibrium.
Having mods play well together without altering progressions or introducing OverPowers is one of the most tedious work you will have to handle as a mod packager.
Bullshit, I've run a modpack and server with GT and a lot of other mods for a long time now. Balance was something that took effort but was well rewarded. In this case, the GT oregen just flat out does not work alongside CoG. I've done what I can to let GT do it's thing and save CoG to do what it does best. In the end I'll end up disabling all of the GT Oregen and recreate in CoG where I have control.
It seems like GT is becoming 'Better Than Wolves' an experience that doesn't tolerate any other mods outside of its creators vision. This is sad. If the answer to incompatibilities is 'you don't need that' than I say bullshit. I want it. I like my nether ores. Yes GT adds ores to the nether, but I like the way it's done by netherores and I intend to keep it. Once again I'll just have to disable the GT nether oregen and recreate with CoG.
I know this is the kool-aid stand, but the answer to every issue is not always 'just drink more of Greg's purple drink'.
Oh and the issue with HarvestCraft is not the Thaumcraft stuff, that I'm familiar with. It's that we get frequent 'Already Decorating' crashes that do not occur when it is CoG doing the Oregen.
Bah, on sober second thought I realize you were trying to be helpful. I apologize for letting my temporary frustration turn into a bit of a rant.