I would think that the average surfer would be more weary of seeing this
Code:
http://hit.sunnydollars.net/in2.php?aid=5083&pid=1&sid=53&tid=1&optid=247&c=A
in the status bar than this
Code:
http://amateurcollege.com/
In this particular case the full URL is actuall more "blind" because it doesn't show the true destination URL at all. Whether or not it makes a difference in conversions I couldn't tell, but i always mouseover my own links just in case.
I think you're right that if a crafty bugger wants to fuck you out of your commision there's nothing you can do about it.