You don't have to put your referral tracker in all links outside of hubpages, in fact at some places you can't (since it's an affiliate link). The benefit for you as a hubber to insert your tracker code where you can is that you will likely get people signing up under you, especially if you are singing the praises of hubpages. You then get 10% adsense and amazon impressions on any hubs they create (taken from Hubpages share).
It's well worth it in my opinion - I have several sign ups that while not prolific as such, definitely know what they are doing and I earn quite a bit each month from their hubs.
So whether you add the tracker or not is completely up to you, but if you leave it out you might be missing an opportunity.