Every forum I have been to has this exact same question posted, with similar replies to this question. My take on this is this: I believe the only niche this is a problem is in the IM niche. And theres no protection. For instance: Lets say Im an idiot..... (up for debate I know)
I click on a masked aff link. I'll look at the destination url opn a new browser type in the url and go sign up for the aff program and by through my own link.
I havent done extensive research, yet I have asked my friends and some family who buy stuff online. And the HAVE NO IDEA what a hoplink is, or an affiliate program. They dont even get what google adsense is. I watched my girlfriend surf one night, she found an adsense landing page about las vegas and happily referered back to it numerous times.
I still think the only place hoplink theft takes place is in the IM niche, probably where most of the theft takes place. So dint think it really matters what extent you go to hide or mask your link, if someone wants it as theres, there isnt anything you can do. Sorry to sound grim, but I believe its the case.