I've tested it by setting up a webserver on my mac. The difference when starting the site from a webclip is, that mobile safari sends out additional requests for the homescreen icon:
GET /apple-touch-icon-57x57-precomposed.png HTTP/1.1
Host: 10.0.2.1
User-Agent: MobileSafari/6533.18.5 CFNetwork/485.12.7 Darwin/10.4.0
Accept: */*
Accept-Language: de-de
Accept-Encoding: gzip, deflate
Connection: keep-alive
Other observed requests are:
GET /apple-touch-icon-57x57.png HTTP/1.1
GET /apple-touch-icon-precomposed.png HTTP/1.1
GET /apple-touch-icon.png HTTP/1.1
You could check for those GET-Requests on the server.
I don't know if this happens everytime when clicking the webclip or only once.