Does it? I can see all 3900 in my account. I just checked and scrolled through them to confirm. Unless you mean a serp. Then yes, they only show up to 1000 results.
"anchor text" ? do you mean "keyword" ? if you only want to check yahoo backlinks then you may try seoserp.com/web_tools/yahoo_top_1000_serps_checker.asp you can find all URL link to your domain or key URL. here a tip for you : the target keyword you may use ( link:keyword )
I would agree that Google webmaster tool and Yahoo site explorer are excellent ways to check back links. However if you want to see how many backlinks you have and what the anchor text is this is the best tool I have found http://www.linkdiagnosis.com/ takes a while to check your site. Im not going to give anything away but this can be a very powerful tool for spying on competation!