I believe not all of them have them... some are direct downloads and some have the wrapper.
I don't think the wrappers are going away at least I wasn't informed of it. I get some clarification and ask the Download.com team.
Today I was downloading softwares from your site, and I have found that most of the downloads that I did, was available via CNET Secure Download, without any wrapped installers. Are you in the process of removing wrapped installers for your downloads? Or is it just because freeware authors compelled to remove wrapped installers for their softwares. Till recently, all the softwares that were available without wrapped installers were only available via "Direct Download Link" but now they are available directly through "CNET Secure Download" . What's happening?