On one hand, long and ugly affiliate tracking links are a straight giveaway to people that you want to sell them a product (and people may be uncomfortable clicking on them). Therefore, making your link shorter and "nicer" looking will it give a more professional appearance. One of my favorite plugins for making links look "pretty" is the Pretty Links WordPress plugin.
If you have pop-ups and optins on every page, I would have to think that it would be a lot harder to convince someone to link to it. Especially since the pages where you have your optins (and probably receive the most traffic) are probably the same pages that you have your best content on as well that you'd be hoping to pitch in your outreach campaign.