The 'subid' field exists so you can manage multiple sites under one account and get distinct tracking/reporting on them separately. That's it's only purpose. So it's not so instrumental in core tracking, but rather, a subfunction of the reporting process. (Sounds like I know what I'm talking about, right?)
I considered using it, but realized if you want the benefits of fully in-depth reporting for different sites, you're better off creating separate accounts.
That being said, it's not going to impact your reporting or tracking if it's not there, or if it's a "0" or a "42", which, if you've read The Hitchhiker's Guide to the Galaxy, you'd know is the answer. But I digress...
Don't just take my word for it. Try it out - that is, remove the 'subid' part entirely - with any link you have, whether text, banner or searchbox, etc., the next time you make a purchase of your own. You'll see. (There are only a couple of core variables in any affiliate URLs essential to tracking, and 'subid' is not one.)
As to the source of your drop-off in success, you might want to graph your conversion ratio for product links individually by merchant over time. Looking at trends visually helps me spot cause and effect.