Yes. If you are using luxuries anyway, having more black hat citizens is an improvement. And you get them by founding more cities. That doesn't mean that it is a "bug" that 2 luxuries make them happy, just that having more cities isn't always strictly worse for happiness. Perhaps one of the skills of Deity level is recognising this, and planning accordingly.
The AI aggressiveness thing was generally considered a "bug" since classic didn't have it, and people would actively choose to play the 'inferior' version of the game to avoid it (it would also let them play deity+ levels as well). Perhaps it was poor design choice, but that's different than a bug. The "key civ" mechanic takes your power rating and assigns you a 'key civ', white if you're pathetic, purple if you're supreme. The further ahead you are in research compared to your key civ, the more your research costs. If your key civ is missing, that counts as 0 techs. Usually, GOTMs were played using the purple civ to circumvent this. Is the key civ mechanic a bug? I doubt it very much. It seems deliberate, just poorly thought out. But that's civ 2.
I'm not against changing 'deficiencies' in Civ II via patch, as long as they're optional. In fact, these days most of my civ time is spent writing Lua code for the TOTPP version of the game.
Maybe I'm just pointlessly arguing semantics. But to me a "bug fix" is something you could reliably predict that most people would want to change, or which is obviously a mistake, while a feature change is something that people may or may not want, perhaps varying from game to game.