"It's time to move on and it's a good time to do it when the opposition isn't that good," Thomson was quoted as saying in the Herald Sun and Daily Telegraph newspapers.
Top-ranked Australia host bottom-ranked Bangladesh in a two-Test series in Darwin and Cairns next month.
"What's he going to prove if he plays Bangladesh? Who cares if Steve Waugh gets a hundred?
"If (uncapped 22-year-old) Michael Clarke gets 100, I am sure everybody would be happy to see that or somebody else," the former pace bowler added.
Hookes, now a television commentator with Thomson, said World Cup-winning skipper Ricky Ponting should be also be handed
"I can't see any point Steve Waugh playing Bangladesh. He won't get a hit for starters," Hookes was quoted as saying.
Hookes, who has been a constant critic of Waugh, said the 38-year-old's presence in the middle order would give it an ageing look alongside Damien Martyn, 31, and Darren Lehmann, 33.
Waugh averaged 75.33 as he led Australia to a 3-1 victory in the Test series in the West Indies last month.
The former World Cup-winning skipper, who was overlooked for this year's Cup defence, watched on television from Sydney as Ponting led Australia to a 4-3 win in the one-day series against Brian Lara's West Indies which ended on Sunday.
Waugh has played a world record of 160 Tests and hit 30 Test centuries, behind only India pair Sunil Gavasker (34) and Sachin Tendulkar (31).
