It is almost impossible to find a laptop with more than one HDMI connector. I would advise you find a laptop with at least one DisplayPort (even if it's miniDP), and then another connector may be HDMI or VGA.
You shouldn't have difficulty finding laptops with HDMI and VGA. I am however kind of wary of their behavior. It is likely that most will enable 3 monitor configurations, but some may only allow one additional external monitor. I highly recommend asking the vendor, or figuring out a way to test it before purchase.
As for 2 HDD bays, there are some out there, but you really need to hunt for them, they are typically found on higher end models. My GF has an Acer laptop with 2 bays.