Are shaders more efficient than manual pixel replacement?

I am building a real time strategy game where each unit is a sprite. Some pixels of the sprite can have their colors changed. Whether a pixel can be color changed depends on the hue of the pixel (in hsv). I have written a script that manually replaces the pixels within the sprite texture. When there are many units in the game, the performance slows down.

Would it be more efficient to use a shader instead? What makes a shader more efficient? Thanks in advance.