I don't think the ultimate theme of Deltarune will be "There is no freedom in video games and your choices don't matter", I don't think Modern Toby is pessimistic enough to do that. However, I think that will be the theme of the weird route.
Undertale starts with a simple message: In this world it is kill or be killed. The pacifist ending, which is the good ending, rebukes this message and it is replaced with Try not to kill and try not to be killed.
However the genocide route of undertale instead embraces this message, in this world it is Kill or Be Killed. You kill everything in your way, you get so strong nothing can hurt you, you embrace this way of thinking, You kill so you can never be killed, that is LOVE.
Deltarune starts with a message, "Nobody can choose who they are in this world" / "Your choices don't matter." This game is about proving this statement wrong, the normal route will likely end proving that your choices do matter and you can choose who you are, you can choose to be a good person, all that.
I propose the weird route will do the same thing as the genocide route, it will run with the original theme, that there IS no freedom. In the weird route you are taking away other people's freedom, Noelle has no choice, Kris is just a puppet. And I think that maybe there truly only IS one ending to deltarune. Because in this world, your choices don't matter, right? So why WOULD there be a second ending?
The dark bead says:
>"Broken off, but still locked."
The weird route is just another path, it is an intended part of Deltarune, Toby coded this in. There is no freedom, you aren't breaking the game despite how much the weird route tries to pretend you are, you are playing something Toby intended. And even then, bug and glitches in games are still contained to the game's engine. You can never truly be free in a game, there is always a limiting factor.
The weird route will be the Halloween Hack 2 theme wise. It is impossible to be truly free in a game.