Does the new Wagon R Duo have the option of converting/ enhancing from the LPG option to the CNG option

no

The biggest consumers for CNG r traditionally commercial vehicles, taxis & autorickshaws -- which will be the case for a long time to come. But with a choice in cars that run on CNG/LPG, we might be seeing a slight degree of change.
So if u want to buy a CNG or an LPG car, what choice do u have? In CNG, u have the Chevrolet Optra, the Mitsubishi Lancer & recently, the Tata Indica & Indigo Marina. Ford India too will get onto the bandwagon, with a CNG Ikon scheduled to be introduced in the northern & western parts of the country - where the CNG distribution infrastructure is established -Probably by next month
And in LPG, u have the Suzuki Wagon R Duo (as u have noted) & Omni, while the Tata hatchback & estate will also be available with LPG options.

Coming to ur question, yes ,You can now convert any petrol vehicle to CNG or LPG. But the difference now is that manufacturers themselves r offering these as options. Earlier, u had to go to an authorized kit installer to convert ur car (and cross ur fingers hoping it would be safe), but now, u can opt for it at the dealership level itself. No, it still does not mean factory-fitted, it is an aftermarket fitment.

Let me explain. Ignore the Wagon R Duo/Omni, which r the exceptions to the rule here, as they r the only cars on sale now with a factory-fitted LPG kit. The rest of the cars - the Lancer, Optra, Indica & Indigo Marina - come with CNG options; which means that the installation of the kit is done at the dealership level, & it is not factory fitted.

Hindustan Motors, General Motors & Tata Motors have tied up with CNG installation specialists who will fit the kit at the dealer end & deliver the car.

Yes!. It is possible to convert a Wagon R from LPG operation to CNG operation. But it is going to be expensive. U will have to remove the already installed LPG kit & replace it with an authorised CNG kit for Euro 3 wangon R. The cost is likely to be in the range of rs 40.000. Allso the car will have to be presented to the RTO fpor amendment in the RC.

no

All cars can be converted to CNG at the cost of losing manufacturers warranty. CNG kits are retrofitted but are expensive options driven mainly by regulations (Delhi Taxis).

Expect an Indian manufacturer to develop an engine actually meant for the combustion characteristics of CNG. Soon.

Not from manufacturer.