I'm a bit confused about the whole disc/cartridges thing. Are the glitches existing only in the narrative? How does affecting the cart/disc affect the comic in-universe?

Homestuck is a story- In-Universe I mean, the fact Hussie is a character and how he interacts with Caliborn, the Glitches, the panel stuff, Homestuck in itself is a bizarre mix of a Narrative that takes elements from Video Games, a Theatre Play and a CYOA Comic. As we see when the Cartridge gets stuffed with Stardust, these glitches begin manifesting physically in the Session, and similarly, albeit not physically, Scratching the Disc makes us lose the ability to play games and eventually obscures what’s going on within the story entirely.

So yeah, the Cartridge and the Discs can have physical effects on the Session itself, even though we only see the former actually having a direct impact.