Allen, 11th-placed Stoke's joint top scorer with six goals, has been on the sidelines after suffering a hamstring strain in a 2-1 defeat to Liverpool earlier this month. Whelan missed the 2-1 victory over Hull City last weekend due to illness.
"We're hopeful. We'll check again today. They came through training yesterday and we'll see if there's been a reaction," Hughes told in a news conference.
"Glenn was really poorly for four or five days. He wasn't in a great place but he's come through that and should be over it.
"Joe's the one we're more concerned about. It's a hamstring and only 10 or so days so we'll have to be a little bit careful."
Hughes said striker Bojan Krkic still has a future at Stoke despite having moved on loan to Bundesliga club Mainz 05 in January in search of regular first-team football.
The 26-year-old Spain international, who has three more years on his current deal at the bet365 stadium, has failed to score in his seven league appearances with the German side.
"Bojan is our player. He got a bit frustrated in the end and I allowed him to go because he wasn't playing here," Hughes added.
"It hasn't really worked out for him, it was probably the wrong team - but he's still with us and there's every chance he'll come back in the summer."
Stoke, currently 11th in the league, could inflict a significant blow to the Swansea's top-flight survival hopes. The Welsh side are two points adrift of safety and have lost five of their last six games. (Reporting by Hardik Vyas in Bengaluru Editing by Jeremy Gaunt)