Is your traffic source & volume the same or has some other factor changed besides just the shielding of your links?
I think this is a great idea. This will keep those evil toolbars, malware and scripts from changing the hoplink on the fly. It doesn't matter if you redirect or "encrypt" your links via PHP. Those toolbars sit in between the network connection and the browser section and watch for affiliate links that float by. They either strip them or replace them with their own. Thanks Clickbank ... now fix your credit card processing.