Hello, the crate walking non playable characters have annoying weird walking animations, Is there a way to remove these NPC? Modding or removing the game files?

Its better to remove them rather than let them exist, so far they have no impact to the gameplay or story whatsoever. Just like additional bytes taking up precious gpu power.

https://www.youtube.com/watch?v=8CiFNQO_igw

Yeah, I don't quite understand how comes they're not fixed already, or at least removed temporarily (feel free to make it a menu option.) Do they even work properly for anyone? I wonder how rare this bug is...

I think we all have this bug, it is strange it has not been fixed, looks really stupid. Some say its supposed to be a easter egg, related to monty python?

I have personally seen this bug many times.

Have the latest patch resolve this issue?

Yes.