Not to my knowledge. If anything, HTTP downloads are more flexible for deploying packages, especially over wireless connections. Search for HTTP on JAMFNation and you'll find a lot of discussions on the ups and downs with implementation. Personally, I found making the switch from AFP to HTTP rather straightforward.
I've installed and configured many JSSes for clients.
I try to use http whenever possible. The big pro, as mentioned, is resumable downloads. The con is that http downloads are slower than AFP or SMB ones.
If your JSS is public-facing you most definitely want to use http, not exposing AFP or SMB shares to the Internet. Some ISP's by default block the mounting of SMB shares over the Internet...