It would be understood to mean more chocolate from a bar (or possibly bars), though "Do you want (any/some) more chocolate?" would probably be more usual.
Compare with:
Do you want another chocolate bar? (another whole bar) Do you want more chocolate bars? (several more whole bars)
If you're talking about some countable thing, use "more of": "Do you want more of this chocolate bar?" You're offering to continue to share the bar. If you don't want to share, say "Do you want another chocolate bar?"
If you're talking about something non-countable, use "more": "Do you want more chocolate?"