What can hinder their performance next season is if their key players move to a bigger club, but if they don't then it means that Atalanta will still be able to come up with their outstanding performance. However, it does not mean that because you performed superbly this season means that you will be able to do the same next season. This is because clubs will want to improve their squad by bringing in new players to strengthen the quality of the club.
We have seen it in some clubs whereby, they win the league this season and did very bad in the next season. Napoli is a typical example of such club. What matters is that a strong club should keep up to its quality at all times, and that is what will make that club to be counted among the strongest clubs. I hope to the best of Atalanta next season.
Have you check Atalanta scored sheet this season? They push their self to the top 4 through collective effort of individual players, there isn't just a single player that is the best, if you check individual stats you will see that even the guy that did hatrick Lookman was having 5 goals before that match prior to that and yet he had 44 appearance this season but luckily piers through Leverkusen thick skin and broke their winning streak of the season.
As long as Manchester City, Barcelona, Real Madrid, PSG, Bayern Munich, and other top teams are present in that tournament, they can't beat all these clubs easily, not this way and just like the way you have said, there is high chance their performance might reduce next season, they only got away with Europa trophy because if Leverkusen carelessness.