Right now? it's because vichan, the codebase that lainchan is based on, doesn't support markdown AFAICT. Why hasn't somebody implemented it? Probably because there are relatively few people working on the codebase, which (by the way) is a cesspit, or so I've heard from those who use it.
If it does support markdown, than it's just that nobody's bothered to add support for it.
and then do a bunch of other things to deal with the differences between the chan markup format and markdown.
Alternately support for [latex][/latex] and [markup][/markup] blocks could be added using the existing regex engine to do the replacement, along with a custom callback or similar logic to the existing [code] tags.