It is difficult to tell to what extent Liljegren's play was impacted by his illness and injury. You are right that there could be more to his stagnated development than the mono.
Below are a few reasons why a lot of us are optimistic that it was his illness and injury that stagnated his development rather than something more.
1) The high level of skill and hockey sense he showed as a 16 year old in the SHL, is not something you just lose the next season when you are playing at the same level. Often when players plummet in the rankings from one season to the next it is either, because they have moved up a level and their skillset doesn't translate, or there were players carrying them that are gone. Neither was the case with Liljegren.
2) The effects of mono coincide with some of the observations that the scouts were seeing (decision making).
3) The WJSS (although a short summer tourney) did clearly show against quality competition that hockey sense criticisms were being overblown, that he is in fact sound and competent defensively, that he is dynamic offensively, and that he is beginning to show the form he had before the mono and hip injury.
4) He faced a tremendous amount of adversity during the season other than just the mono, which included: being bounced around multiple teams/levels, hip injury, tire fire of a team in Rogle who was facing relegation, attempting to return early from mono, and the weight of draft year expectations when everything seems to be going wrong. That is a lot for a 17 year kid to have to deal with in their draft year.
5) It seems due to limited viewings with all that had happened, scouts put a lot of extra weight into his performance at the U18 tourney, in which he didn't dominate, but in fairness, played on an offensively challenged Swedish team and had just come off a hip injury. This I believe ensured his fall on draft day.
6) There seems to be a lot of revisionist history as far as his scouting reports go. Reports from his 16 year old D-1 season rave about his hockey IQ and hockey sense, and then in his draft year around January some scouts start to question it. I don't think a player just loses hockey sense. There is also revisionist history as far as his Hlinka performance goes. Reports at the time of the tourney raved about his performance and then months later McKagg and a couple of others change the narrative and said he played poorly (I question whether they even watched it).
7) Leafs management and scouting is pretty savvy, and Mark Hunter seemed very confident in the pick and his illness was the culprit for his stagnated development.