Yes, there is a big difference between these two words:
In this context, "roughly" means "approximately" e.g. "It's roughly five miles away."
"Hardly" does indeed mean "almost none" so you can indeed say "I can hardly understand him." But be careful - it's an adverb so "I can hardly understand a conversation..." sounds a bit odd. You might want to find an adjective to describe the conversation instead: "His conversation was unintelligible to me."