That's partly true, but if you SSH in you're able to access the standard unix folder structure which at least gives you a semblance of organisation and control, even if individual files aren't always named in easily accessible ways.
"IPhone Explorer" only show's the entire content If the device Is jailbroken
If jailbroken:
U have acess to the entire iDevice, suports drag'n drop. (REAL QUICK Transfer speed)
Speeds up installation process, just to drag the ipa/deb file into your idevice and install It from there rather the using SSH's slow tranfser speed.
Use It with care, u can really mess up your iDevice moving around things.
But the main question was If there was a APP doing this!
All my iDevice's are jailbroken and Im using "iFile" to browse the entire content.