Theatre
The school musical is an allegory for the way that many queer teenagers find comfort in theatre and music programs. These programs are often welcoming for queer students in ways that other programs are not, so Simon and the other LGBT+ students at his school are very comfortable participating in these programs. Their comfort reflects the larger world outside of the novel and the experiences of students similar to them.
The party
The party that Simon and his friends go to is a symbol of their coming of age and departing childhood. While they had been known as goody-two-shoes type students for the majority of school, going to the party and drinking is their first "rebellious" moment in high school. It acts as a symbol of their development and entry into adulthood.
Secrets
Characters keep secrets from each other throughout the novel, making it a prevalent motif. Simon is obviously hiding his sexuality, but Leah is hiding her feelings for Nick (and possibly Abby), while Simon's older sister is hiding her new relationship from her family. This motif of keeping secrets represents the time of adolescence and young adulthood, when young people are trying to figure out their lives and might not feel comfortable sharing details about those lives with the people around them.
Blue and Simon's Relationship
Blue and Simon's online relationship acts as an allegory for the many queer teenagers who are in online relationships because there are no other LGBT+ youth in their area. They may be the only openly queer student at their school and end up looking for a significant other online, or may only feel comfortable in an online relationship. Either way, Blue and Simon represent, and act as an allegory for, the many other queer teenagers in their same situation.
Simon's friend group
Simon's friend group experiences some tensions when Abby moves -- Leah feels ignored and the balance of the group shifts somewhat. This acts as a symbol for the disruptiveness of teenagers' lives, where their relationships shift frequently and often cause stress.