You're right - the site has an obscure algorithm which sets the difficulty depending on the size of the puzzle and the number of black squares. So when you start designing your own Hanjies, you'll find adding an extra column or row or one or more black squares changes the difficulty dramatically either way! There must be an optimum number of squares for a really high score, but I haven't worked out yet how many.
The highest score I've seen is a maximum 4,200 for a 25x25, the lowest a maximum 30 for a 5x5, but other people might have seen better or worse.
It's best just to design something you think people might like!