You are so right. I tested my encoder SW to ensure that wouldn't happen. My platform can handle up to 250 KHz inputs, which is more than sufficient for my ELS. 100KHz is the max bandwidth of my spindle rotary quad encoder. (And that 100 KHz corresponds to 5000 RPM, which I will never do, since my chucks can't go that fast!)
Linear encoders, at least the scales I have, are much slower. I have 1um Z & X scales on my lathe, but won't run into an issue as I will never traverse that fast on feed or threading. (It would scare the heck out of me, for one thing.) For fast travel on a mill, or CNC, I'd want to redo the math to ensure myself there wouldn't be any issues. If you play in this domain, you need to check and double check things to avoid BIG problems.