A Box is definitely ideal for carrying a lot of skis, and one like the Thule ascent 11 is a great box if you are on a budget.
However to answer your question, no, the Yakima Fat Cat 6 is not a lot longer than the Thule, if at all. You will not get 6 pairs of super fat skis in it. You could probably get 6 pairs of 90mm waist skis in either. The Thule rack does not usually come with locks included in the box, so you might want to confirm they will include the locks with that.
The Thule rack has thicker, higher quality rubber and is good if your skis are thick (more important for carving skis that have riser plates). It is much faster to install and remove. The Thule rack however, even if you have locks, leaves its mounting bolts exposed. Someone could come with a torx bit and remove the whole rack with the skis. The Fat Cat is easier to use with gloves. It is also more secure against theft if you buy the lock cores.
If I had to choose I would go with the Thule. No matter what, leaving your skis exposed makes them prone to theft. For the extra money you spend you wont get much more with the yakima. If you are worried about transporting 100mm+ waist skis, or the security of them, get a box.
hahahaha i didnt need THAT in depth of an explanation, the vagina isnt really a goddamn box... and i sure as hell dont know why id stick my nose in it.- Evan.S