I haven't noticed my Indo friends using the phrase often, it sounds incomplete somehow. Cherry is spot-on with advising 'apa kabar' as the better option.
I checked around some blogs to make sure, and "bagaimana kamu" does turn up as an incomplete sentence: eg, "...bagaimana kamu mengerti" ("...how you understand").
Kamusku punya: "bagaimana kabarnya", 'how are things' (how its news) dan "bagaimana dia sekarang", 'how is she now'. That may indicate your question could still be understood, but from my searches I don't see it commonly used that way.
Keen for a native speaker's input here! :)