Yeah that's why lit.sh and most similar tools have a mode to output a version of the file with the markdown commented out except for code blocks. This lets you pipe it into any tool and get output with proper line numbers, analysis, etc.

VS code is getting pretty smart about code notebooks too, it has native support for a few different formats of markdown + code blocks (hydrogen, jupyter, etc) and applies all the right syntax highlighting, analysis, etc. to each block automatically.