So 3 reasons:

1. Gamma correction - old school tube TVs work differently than modern LCD/LED screens. Specifically in the way the pixels represent color intensity. With modern screens, there is a mostly linear relationship between the pixel value and the actual color being seen so red 200 is twice as red as red 100. With tube TVs there was a curve, so red 200 might be 3 times as red as red 100, so you'd need to adjust the value down so that it looks right on the screen.

2. A lot of animation was done by hand - a lot of older animation was drawn on physical media, photographed, then assembled into a video reel. This means that the physical color palette used was restricted to what the artists had available at the time. The process used today is almost entirely digital and software can create basically any color you could ever want.

3. Style - in a lot of cases, the darker coloring was a stylistic choice. For example, scooby doo has very dark coloring to add to the mystery/horror atmosphere presented by the show. This is still done in some modern cartoons & animated shows.