What you are deleting is a copy. So when you resync itunes will do one of two things- 1. sync the apps that are still in your apps folder now, which means you will have two of some apps. Only one will be visible. So space will be taken up by an unusable app. Or 2. it won't sync the apps that are still in your folder because it sees them as already there, even though you can't see them on the springboard. Either way it will just be better to take the extra five minutes and use ssh to delete them before you sync. If you have any more questions just post.
update -
I deleted all the apps via SSH.
Synched with itunes
all seems ok at this moment. All possible apps back, phone seems fine.
I guess the ultimate mystery - why did this happen, and how can I (we) avoid it in the future?
all the best !