There appears to be many different colours for lakes in HoI4.
Some of the variety may be due to bleedover from the border lines.
One consideration is to have a consistent color for each terrain feature, so that the customers' eyes become trained and accustomed to interpreting that one colour for that one type of terrain.
Granted, there are more important issues than debating if lakes should be represented by a single colour or multiple colours.
Different map views might demand that different shades or colours be used in order to be consistent with the overall theme of the map view.
It may be that a variety of lake colours is the best method for conveying information to the customer.
But there are quite a few colours used to represent lakes.