Thermal Noise Sampling on Capacitors
You calculated the signal power incorrectly (the noise calculation is correct). Signal power is half of square of the signal voltage:
$$S = \frac{V_{in}^2}{2}$$
In the first case:
$$SNR = \frac{V_{in}^2}{2}/\frac{kT}{2C} = \frac{V_{in}^2C}{kT}$$

In second case:
$$SNR = \frac{(2V_{in})^2}{2}/\frac{2kT}{C} = \frac{V_{in}^2C}{kT}$$
Thus it is same in both cases.