Please don't confuse real life physics w/ narutoverse physics. Many fictional worlds in manga and anime have ninja's paralyzing opponents by pinning their shadows. Though it's possible it could be genjutsu, I have seen no confirmation of it actually effecting the victims chakra. If it does though, it certainly is a genjutsu.
Well if speed is your determing factor, it be pretty much impossible to differentiate since they are all pretty much instant. I submit the strength of a genjutsu is measured by 1)how unsuspectedly it can be caste, 2)how hard it is to avoid, and then 3)how hard it is to break. If you agree w/ that then I think chakra rods rates pretty high in factors 1 and 3. However not so much in 2, since that depends on the speed and reaction time of the user and victim. To compare KA is unmatched in all 3.
Perhaps the shadow may have a mass. But there are all sorts of things that affect peoples chakra that are not considered genjutsu: Kisime's Samahada, Hashirama's Wood Dragon, Preta Path etc.
Well 1) doesn't work for the rods since the enemy have every reason to dodge it. It is not unusual for sharp objects to be drosed in poison and many ninja would just assume that no matter what it is best to dodge the rods. From an unspecting ninja's point of view, if it hits, he could be killed instantly, poisoned, incapacited, exploded with a hidden tag etc.
So no real element of surprise here.
2) Koto and Tsukuyomi are very hard to avoid. In fact Koto doesn't even need eye contact as evinced with Danzo.
3) agreed, it's very hard to break. But a poisoned spear would do more or less the same trick: affect someone such that they become incapacitated.