Reports emerged before the A-League champions' 1-0 loss away to Melbourne City on Sunday that skipper Smith was set to leave Suncorp Stadium, despite being under contract until 2016.
Thijssen was unable to provide an update on the centre-back's immediate future, but the Dutchman insisted he wants to keep the veteran.
"If he goes, it's a pity for the club," he said.
"He's important in defence. If he will go, you miss another important player.
"I cannot talk about it, it's not on me. That question you have to ask the club. I don't hope that's the case, of course. He's important for the club, we miss already enough players.
"You always hope as a coach that you can keep your better players."
The Roar struggled to create chances against City, Thijssen attributing the problem to overreliance on Henrique, as well as the absence of Thomas Broich, who underwent ankle surgery last week and will be sidelined until 2015.
"We rely too much on our Brazilian striker, he's our goal-scorer," he said.
"It's easier to defend if you have one player who scorers goals or a lot of players who score goals. We lost a striker (Besart Berisha) to (Melbourne) Victory who scored a lot of goals.
"Thomas (Broich) was for us also very important, who works very hard and gives the example. It's a lot easier to put the pressure on other teams with a player like this."
The Roar have been linked with several available defenders following news of Smith's potential exit, but Thijssen believes reinforcing the frontline is a more pressing concern.
"A goal-scorer is welcome of course, because it makes for the team a lot easier, if you put the ball in the net. I'm quite happy with our defenders, I think the young boys are doing well."