A not-so-quick Too Long Didn't Watch, because I still wanna share my findings from this analysis with people who don't want to or can't watch the video:
There's a set of themes that I named "STRIX", which play in a serious tone when it's Twilight doing his spy stuff, but when it's Anya looking up to what a cool spy he is, they play in a comical manner by a loud and slightly off-tune recorder. Perfectly symbolizing the Serious Spy and the Little Hopeful Girl who wants to be like him respectively.
There's two different leitmotifs for Yor and the Thorn Princess. However, the latter one has appeared in scenes where Yor is still herself, just putting her assassin physical skills to use, like when she parkours her way to Eden to give Anya her gym clothes. Or when she gets drunk and kicks Loid's ass in episode 5.
Yor's leitmotif is the same melody from the lullaby she sings in episode 24, the one Twilight remembers his mother singing to him.
There's two melodies connected to family moments. Usually they are played side by side, but near the end of Yuri's first visit at the Forger house, the song starts playing as Loid offers him a place within the family, then cuts off as Yuri rejects him.
The second "Family" melody and one of the "STRIX" themes have similar musical elements. The Forgers are, after all, a family that was created as part of Operation Strix.
The music for Damian emphasizes his depth and his potential for growth.
Twilight as a character doesn't have a leitmotif - leitmotifs are used to represent a character, a dynamic, a situation, etc. and the lack of a distinct theme for Twilight adds to the element of him not having an identity. While his Japanese voice actor does a great job using different voice timbers for each facet of the character - Twilight, Loid, and the real man behind it all - the character is still biased. The background music is an omniscient and objective narrator, so it doesn't enforce specific interpretations on the character. It allows us our own.
The only theme I could find that could be, potentially, the theme of the man behind all the masks, is the melody that plays in the first episode, when he remembers the reason he became a spy: to build a world where children don't cry (a very important character moment, if you ask me). As the series progresses and we, hopefully, see more of his real self coming through, I'm curious to see if they'll use this melody as his leitmotif.
BONUS ROUND: the insert song that plays in the "Loidman" scenes is a rock cover of Bondman's theme. Even the music was in on the game.