Firstly, welcome to Dakka!
Next,
40k rules questions go in the
40k You Make Da Call sub-forum.
A Two-Handed weapon is only a single weapon, and prevents the model gaining the +1A benefit of having a second melee weapon.
Specialist weapons also prevent the model getting the +1A bonus unless both weapons are Specialist.
Here are some examples:
2 normal close combat weapons = +1A
2 Specialist Weapons = +1A
1 Specialist and 1 normal
ccw = +1A when attacking with the normal weapon, but
not when attacking with the Specialist (Specialist only kicks in when you are attacking with that weapon).
1 Two-Handed weapon and 1 normal
ccw = As for Specialist, +1A when attacking with the normal, but not when attacking with the Two-Handed weapon (I know, it's wierd).
Now, here is what you might be getting confused about - a Thunder Hammer does
not have the Two-Handed special rule.