No you're just barred from being able to hit anything when you run. Like when a cliff racer shows up for the ten thousandth time and you can't hit it because you were trying to get somewhere slightly faster.
Scrolls and enchanted items (rings, clothing, etc.) don't have a hit or cast chance, so you can kill the ten thousandth cliff racer with the ten thousand scrolls of Drathis' Winter Guest that you can buy from Arrile for extremely cheap since he's guaranteed to sell them at a reduced price if you gave Fargoth his ring.
If you're playing a magic character with at least 50 in willpower and decent restoration you use restore/absorb fatigue spells very reliably even with 0 fatigue. Or just set a mark in front of the Shrine to Stop The Moon in Vivec and get the 500pt levitation buff that makes it so that you not only move faster but you also won't be expending any fatigue since it puts you in the walking animation.
If you don't wanna use any magical solutions at all you can just find a chest to leave all your extra shit in and make sure you use less than 50% of your encumbrance when you're venturing somewhere. You'll regain your fatigue faster than the enemy will have a chance to even hit you if your endurance isn't shit, and you'll kill them faster as well.
Or you can just keep running. I try to avoid using the Boots of Blinding Speed so I always level up speed first, and after awhile you will just outrun them. Or outjump them, in my case.
tl;dr fatigue isn't perfect and I wouldn't have designed it to drain so fast, but it is very easy to circumvent. Starfield and other Bethesda titles would probably benefit from having a stamina bar that isn't so fucking boring and static. The CO2 meter is such a joke from what I've seen, I'm sick of limited sprint bars that just exist to make traversing these boring ass worlds take even longer in a way you can't circumvent.