If I want to run navy as my affiliation do I need to have at least two navy objectives in my deck or will one do? (Or zero)

You do not have to have a single card that matches your affiliation. The only time it matters (rule-wise) is when an objective says "xxx affiliation only."

You are only restricted when choosing an affiliation when you choose an objective set that says it is a certain affiliation only.

The Ultimate Power (Objective set 28) says Imperial Navy affiliation only. If you use this set, you would be required to use the Imperial Navy affiliation, you you would not be able to play any Sith or Scum and Villainy affiliation only objectives.

If you don't have any objective sets that require you to play a certain affiliation, your best choice is to use the affiliation you have the least objective sets of.