Kelly also said Louis Nix III is questionable after not traveling to Saturday's game because of knee tendinitis.
Notre Dame's makeshift offensive line protected Tommy Rees well against Air Force.
"When you're playing an option team, as I said to you last week, it's really about getting out there and getting acclimated to what you're going to see," Kelly said during a teleconference. "If he has a few days of practice where we really like it, I could change that. But I would say it's questionable right now."
Ronnie Stanley also left Saturday's game, but Kelly said he was not concerned about his status moving forward.
Stanley and Watt were the latest injuries to an offensive line that was dealt a major blow earlier this week when right guard Christian Lombard was shut down for the season after having surgery to remove a herniated disc in his back. True freshman Steve Elmer started for Lombard but later found himself at right tackle in place of Stanley, with Matt Hegarty moving up to the right guard spot.
Romeo Okwara would appear to be the next man in at the No. 2 cat linebacker position in place of Williams, who actually started against the Falcons as a down lineman. But Kelly is keeping his options open.
"Well, we lost him really in the first couple drives. We played Romeo quite a bit," Kelly said. "We played Ben Councell. Justin Utupo played very well for us. We got a lot of guys involved."
Kelly sounded less worried about his team not being ranked in the latest AP poll, though the Irish are No. 25 in the coaches' poll.
"I think we're still in a pretty good position as long as we win," he said. "We've got to win more football games. We're only 6-2. I think if we take care of business and win week after week, we've got some quality teams in front of us, I think we're right where we need to be. Just keep winning football games. I really believe that as long as we just take care of week to week, we're going to be fine when it's all said and done."