The
MW's are not blocked, because they happen in a different part of the attack sequence. Basically, when the attacker rolls their meltagun hits, the Crit effects apply at that point before the defender has any chance to use their dice. The rest of the damage, ie. 3, can be blocked normally with a roll of a six but at that point you're rather looking to use it on a normal 6 damage hit.
Specifically:
Meltagun's Mortal Wounds effect is stated as "Each time a friendly operative makes a shooting attack with this weapon, in the roll attack dice step of that shooting attack, for each critical hit retained, inflict x mortal wounds on the target, x is the number after the weapon’s
MW, e.g. MW3."
The sequence for shooting is:
1. Select weapon
2. Select a valid target
3. Roll attack dice
4. Roll defence dice
5. Resolve successful saves
6. Resolve successful hits
7. Remove incapacitated operatives
Since the
MW's happen in step 3, the defence dice do not matter in this interaction. They haven't even been thrown yet