No, I don't think it will replace cryptocurrencies exchanges. Atomic swaps is not that fast. Also, for a trader, cryptocurrencies exchanges it still the the best for them so they can take advantage of any movements in the market.
Atomic Swaps is actually a pretty interesting topic to discuss because of what it can bring to the table but I agree, it would be hard for it to replace cryptocurrencies exchanges for the reason the we all know who's faster. Though losing your funds is a problem.