Stokes and paceman Gus Atkinson were dropped for England's second Test against New Zealand and investigated internally for breaking curfew while celebrating victory in the first match of the series.
British media also reported the pair were involved in a physical confrontation with rugby player Totoa Auvaa, who was attending the same London nightclub.
The incident raised questions over 35-year-old Stokes' tenure as captain, and his international future in general.
One of the faces of England's "Bazball'' revolution, allrounder Stokes toiled with bat and ball but was criticised for his decision-making during a 4-1 Ashes series thrashing from Australia over the summer.
Test rival Lyon opted against weighing in to speculation over Stokes' future as skipper.
"I know what my comments seem to do, and I don't really feel like getting abused on Instagram," he said.
But Lyon hoped Stokes would be on the pitch in mid-2027, when Australia will fight to retain the Ashes with their first outright series win in England since 2001.
"To be honest with you, I'm really hoping this isn't the end of Ben Stokes' career. I've got nothing but respect for Ben," Lyon said.
"He's going to go down as one of the greatest to ever play the game, and I really hope that his career's not finished.
"As Australian cricketers, you want to be playing against those guys, and Ben Stokes is arguably one of the best to ever do that, especially for England."
Former Test captain Joe Root will serve as interim skipper for this week's second Test against New Zealand.
"Joe Root is arguably the best player in the world," Lyon said.
"Nothing but respect for Joe."
Lyon is nearing recovery from the serious hamstring injury he suffered in last summer's Ashes and is hopeful of being available for the home series against Bangladesh in August.
"I'm absolutely flying, I feel really good, really confident. I'm actually itching to get back bowling to a batter," he said.
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