Really, it depends entirely on what you have and what you want. Some go the nuclear restoration route and try to make an engine look brand new, while others are minimalist and simple restore good operation, leaving the original patina as intact as possible as it is a record of the engine's history. There are many who work in the zone that falls between those two opposite approaches.
If you have a truly rare engine, heavy restoration can definitely destroy much of its originality, and thus its value. However, done properly, a good restoration can enhance value and desirability. It can be a fine line that is not always very obvious where you pass from light into shadow.
If your engines are pretty much run of the mill, vin ordinaire, then simply do what you want to make them the way you want them to be.
Everybody has different tastes, but at the end of the day, they are your engines, so only you can know what you want of them!