Yukkuri melting in water itself is kind of hard to believe. Water would weaken their structure, but if the manju stay put, they should be able to more or less maintain shape. Although it's not like they'll be able to move afterward without destroying themselves.
The water bubbling and circulating because of the heat, or stirring, would be more effective to actually break them down in water.
Or, it might be the panic. When in verge of death, they starts moving violently. Or, the paste circulation inside also became faster (like our heart beating faster when in panic) and that's the main factor that breaks the already brittle skin rather than the water itself (that only serve to weaken the skin).
All true. Yukkuri aren't exactly the best conductors of heat, either. The bigger an object gets, the easier the heat dissipates into the air rather than go inside the object.
That's why aluminium powder is highly flammable, but a block of aluminium is not.