The accuracy would be the same, but the second method would be more precise.
Well the term "handful" is pretty imprecise to start with. Let's say a handful is 20 coins. Suppose the fraction of pennies in the bag is P. The distribution of the number of pennies in your handful is F(n) = Pn(1-P)20-n*20!/(n!(20-n)!). This is a binomial distribution.
The expectation value of n (what you would expect to be the mean value of many trials) is 20P, and the variance (square of the standard deviation) is 20P(1-P). The expectation value of p, the fraction of pennies in your handful, is P, and the variance is P(1-P)/20.
Now suppose you take two handfuls, i.e. 40 coins. E(n) is 40P, V(n) is 40P(1-P), E(p) is P , and V(p) is P(1-P)/40. The expectation of p is the same - p is an unbiased estimator of P, which doesn't depend on the sample size. The variance of p decreases with increasing sample size, so p is more precise for larger samples.
In either case, if you did the trial 3 times and took the mean value of p, the expectation would be the same (P), but the variance would be divided by 3.
If you had a source of systematic error, e.g. the heavier coins sank to the bottom of the bag, this would probably be reflected in an effective probability of drawing a penny, P', different from the fraction of pennies in the bag, P. Both your methods would estimate P', so neither would be more accurate.