Yes, of course you should watch Star Trek! That goes without saying, regardless of your interest in Lower Decks.

(But yes, Lower Decks does make a lot of in-joke references. I imagine it’s still funny without them, but you’ll be missing quite a bit.)

BTW, Lower Decks is only one of three(!) animated Star Trek series now. I’ve only seen the first episode of Prodigy, but I get the impression that it might be less self-referential and thus might be a better introduction.