Hi Sisone
As you so correctly point out if a child sits in W-sitting she does not need to use her trunk balance responses. But she will also tend to develop tightness in the fascia lata and related myofascia. And these children develop external tibial torsion - the knee can rotate laterally but not medially. And this is one of the reasons the child does not like sitting cross legged - because thye do not have adequate medial rotation of the knee needed for cross legged sitting. if you as the child where thye are uncomfortable, they usually point to the lateral aspect of the lower leg.
The chances are that if the child has so called low tone she has hypermobile joints and muscle weakness. You cannot do much about the hypermobility - but muscles can be strengthened.
How old are the children you are seeing?
In my experience you need to practise sitting with the legs in front of the body and sitting on a chair.
If you tell me more about the children you are seeing, I can make some suggestions for training sitting.
But to answer your qustion - yes it does affect the child learning to sit erect with comfort and that becomes a problem when the child goes to school. It is also often associated with poor ability to stand on one leg and hop.
Best wishes
Pam