Stealth jump is REALLY nice to have with a roller, since you can just land on someone from seemingly nowhere and instantly take them out. Useful in general anyway considering the amount of times I've seen people(myself included) get targeted or a mine placed at the landing point just because they can see where they are going to be. Especially nice on maps like underpass where people tend to super jump a lot.
Ninja I don't think is actually quite as useful, for starters it makes you go slower which is a flat out nerf, and the invisibility factor itself isn't extremely useful considering squid is a movement/escape option and less of a stealth tactic. Besides, you're rather hard to see in chaotic situations like mid of warehouse anyway, and most of the times when I see people trying to be stealthy they're standing still waiting for their prey anyway. I guess standoff situations like the low ground midpoint with the box on salt rig(wow that description was awful) can be where ninja proves to be useful thanks to how you force the opponent to guess even further as to where you actually are, but that's just in theory and IMO not quite worth the slower speed and valuable upgrade slot taken.