Rumours linking Williams with a move away from the Liberty Stadium have gathered pace in recent weeks, with both Liverpool and Arsenal rumoured to be interested.
Meanwhile, Flores is believed to be a target for Bundesliga outfit Bayern Munich.
The Dane said speculation is an indicator that the Swans are doing something right and admitted they will "have to live" with the stories.
"When there are rumours about these clubs wanting someone from here, it is because the player has done well," The Mirror quotes Laudrup as saying.
"What can I do? I can't call Arsenal and say, 'Is it true?' I don't think Arsene Wenger would answer. We will have to live with these stories – it's part of the game – but it means people have seen what we have done here.
"Ashley has had a great season. He and Chico [Flores] have been a great pair. They are doing great together and I will be unhappy to lose that pairing for next season."
Williams moved to South Wales from Stockport County in 2008.