I.e. navigation says score 2/3 from another players pile. If that player does not have 2/3 do they take a 4?
Is it only when drawing a card that you go to the next number up? One card says draw two ones. So when ones run out I can use that card to draw two 2s, 3s etc.?
Yes and yes.
Does the rule of the numbers increasing only apply to drawing cards and not to scoring, anything else?
Yes - only to drawing cards and nothing else.
The "next up" rule is in the section on drawing cards. It begins as follows: "If a supply pile is empty and you need to draw from it, instead draw from the next higher non-empty pile. This happens both for Draw actions, and for any other effects that cause you to draw cards."
If you look at the official FAQ for Navigation, you will see that it says, "Navigation specifically looks for cards of age 2 or 3. If an opponent does not have score cards of age 2 or 3, you do not transfer any score cards."