Dijkstra's Algorithm
Dijkstra has running time $\mathcal{T}(G) \in \Theta(|E| + |V| \log |V|)$. If the graph is dense then $|E| \in \Theta(|V|^2)$, which means that $\mathcal{T}(G) \in \Theta(|V|^2)$.

A quadratic running time means that a graph with twice as much nodes will take four times as much time to be processed. If $1000$ nodes required $6$ hours, then it is not surprising that $2000$ nodes will take about one day.

As you know, constants depend on the machine you're running your code on, it is therefore impossible to judge the speed of your code having the clock running time as the only datum; however your times strike me as particularly high for a reasonably modern personal computer, I would expect them to be a couple of orders of magnitude lower.