Were there any reasons in-universe and out of universe the Empire didn't use Super Star Destroyers during the events of the Thrawn Trilogy?
The out-of-universe explanation is due to a combination of it not yet being established that the Executor was not a unique vessel - it was not until after Zahn began his trilogy that other authors utilised Super-class vessels, themselves recently retconned to fix the size inconsistencies - and the simple fact that Zahn prefers small-scale tactical military sci-fi to large-scale strategic sci-fi. Another great example of this is his Blackcollar trilogy, which focuses on ground combat rather than space combat, despite the latter being more important to the overall war in the story.
In-universe the retconned explanation has been that Thrawn (scroll down to "Final return to the galaxy"), while gaining the loyalty of the Moff Council, did not actually gain the loyalty of the majority of the Imperial military, which stayed loyal to local warlords. Several of those warlords, such as Warlord Zsinj from Iron Fist and The Courtship of Princess Leia, had Super-class vessels, but the loyalist military that flocked to Thrawn did not. This makes Thrawn extending Imperial control over half the galaxy even more impressive.