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.
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...
None of the loaders work with compressed iso's, only scrubbed iso's. NTFS & FAT32 can have games stored in WBFS files, which are like WBFS partitions but you have one for each game.
FAT32 is currently the best, you can use it for everything. Home brew channel can load apps from it, you can store all of usb loader gx on it too. No sd card needed at all (or you could dedicate it for use with sneek).
NTFS has various issues even with software that tries to support it, usb loader gx documentation for example says that installing a game onto an NTFS partition can fail & corrupt your drive.
The only downside is files bigger than 4gb have to be split, but there is software that does that.