The first method is preferred as you are using all the information in the sample to get more 'accurate' measures of central tendency (i.e., the sample mean) and the spread (i.e., the variance) in your data.
More formally, if $x_i$ is from an unknown distribution but are iid with finite mean and variance then it follows from the central limit theorem that:
$$\bar{x} \sim N(\mu,\frac{\sigma^2}{n})$$
Informally the above suggests the following two 'facts':
The sample mean is an unbiased estimator of the true mean as the distribution of the sample mean is centered at the true mean and
The spread of the distribution is narrower with higher $n$.
Fact 1 suggests that the sample mean will remain unbiased with a smaller sample size (i.e., using 500 instead of 1000 should be fine if you are concerned if the sample mean is biased or not) but fact 2 suggests that the distribution of $\bar{x}$ is 'narrower' with higher $n$ and hence it makes sense to use the full sample of 1000 data points rather than 500 data points. Intuitively, facts 1 and 2 together indicate that the higher the sample size used to compute the sample mean, the lower chances that the sample mean is 'far away' from the true mean.
A similar argument for the sample variance can be made. See the wiki on the distribution of the sample variance. In particular see the formula for $E(s^2)$ (i.e., the mean of the sample variance) and $\text{V}(s^2)$ (i.e., the variance of the sample variance).