All versions of webMAN can mount ISO from NTFS drives if the .ntfs[*] file already exists in /dev_hdd0/tmp/wmtmp.
These .ntfs[*] files are normally created by prepNTFS, multiMAN, sMAN, IRISMAN or the full/normal version of webMAN MOD. Not sure about ManaGunZ.
Notice that only the recent full/normal versions of webMAN MOD can create .ntfs[*] files without the need of prepNTFS.
And only these folders are scanned: "PS3ISO", "BDISO", "DVDISO", "PSXISO", "PSXGAMES"
prepNTFS is needed to scan new content on NTFS drives if you use the lite version of webMAN MOD or if you want to use the additional folders that generate a fake ISO: "VIDEO", "MOVIES", "PKG", "Packages", "packages", "BDFILE".
In summary: For PSXISO/PS3ISO games and DVDISO/BDISO you don't need prepNTFS, but for PKG files or movies (*.mp4, *.avi, etc.) stored on NTFS you need it.
If I recall correctly, mmCM always starts an internal prepNTFS.self (deank's original version) everytime it is launched. So if you run multiMAN, you're also running prepNTFS (but this version doesn't support the fake ISOs).