Regarding what magnets can and cannot do in general google "can magnets do work" and read around a bit. physics.stackexchange is usually pretty good for these sorts of questions. If you have the basics in mind it's less tempting to speculate on what they might be doing in a motor.
Cogging is cogging
Iron losses are iron losses
If you've compared a skateboard with a motor that exhibits cogging with a skateboard with no motor then you can't really conclude anything about the relationship between cogging and drag because you can't separate out the different sources of drag in a motor. All you can safely conclude is: the draggy thing has more drag.
Speaking of drag, kinetic energy is also non-linear with speed (E = 1/2 m v^2). So at higher speed you'd need much more motor drag to slow you down at the same rate as at lower speeds. So when you talk about drag from iron losses being small at very low speeds, the amount of drag required to slow down your skateboard is also small.
Cogging is cogging
Iron losses are iron losses
If you've compared a skateboard with a motor that exhibits cogging with a skateboard with no motor then you can't really conclude anything about the relationship between cogging and drag because you can't separate out the different sources of drag in a motor. All you can safely conclude is: the draggy thing has more drag.
Speaking of drag, kinetic energy is also non-linear with speed (E = 1/2 m v^2). So at higher speed you'd need much more motor drag to slow you down at the same rate as at lower speeds. So when you talk about drag from iron losses being small at very low speeds, the amount of drag required to slow down your skateboard is also small.