1) NTFS can do Sparse-Files.
2) You can also convert your ISOs to .wbfs/.wdf/.ciso with the right apps (for example with Wiimms WBFS-Tool).
All these files will result in the smaller game Image (I guess this is what you meant with "compressed"). If the loader supports them, this is another question. CFG-Loader (and as far as I know GX too) supports .wbfs and Sparse Files. .ciso is only supported in uLoader, but uloader doesn't support NTFS, so they aren't a solution for you (also, the fileformat isn't that nice). .wdf is a great format, sadly currently no loader supports it, but it's being rewritten, and soon the loader should support it too.
Summary:
Sparse-Files and .wbfs-Files are supported by GX, CFG-Loader and (probably) also by WiiFlow. So yes, you can store compressed games on NTFS. Which one you'll choose is your decision, I would go for .wbfs, or if you have some time, I would even wait for .wdf. But that's only my opinion...