Confirmed. The problem becomes visible on an NTFS disk, on the Mac, when the files are copied in Windows while MacDrive is interpreting the originals.

Summary:
1. MacDrive in Windows misrepresents c-cedilla and i-umlaut (and others) when reading Mac HFS+ disks.
2. Copying operations that end on an HFS+ disk in Windows using MacDrive are OK on the Mac. It seems to be ok at translating back from the misrepresented accents. Or Mac OS simply understands the messed up names when it reads the HFS+ volume.
3. Copying operations that end on an NTFS disk in Windows using MacDrive will prevent Mac OS from seeing the files with the misinterpreted accents. It doesn't matter if you're using the built-in NTFS read-only driver, Paragon NTFS or NTFS-3g.