"100%" chance to hit can roll a miss, but it won't very often. The vast majority of times it'll have an actual miss is because it's not aiming at the target. This is an extremely common problem. There's a tiny place where the shot aims for, and a good fraction of shots travel along a line that would intersect that tiny place that the weapon is aiming for, and it's about the size of a 9x9x9 voxel cube. The fraction of shots that intersect this target area is similar to the accuracy as a percentage for most values, especially anywhere from "10%" to "90%" accuracy. Thus while it is not an actual percentage chance to hit, you can pretend it is in your head and your results will not significantly vary from that, provided the target area is inside the hitbox of what you're aiming at.
Sometimes (way too often, in fact), the target area that the soldier aims for is partially or completely protruding from the hitbox of the thing you told them to fire upon. This is especially common when shooting units, as their vanilla hitboxes are a fairly narrow cylinder. If your soldier has greater than 90 applied shot accuracy, their shot trajectory will generally intersect with the small target area they elect to fire upon. If that target area is within the unit's hitbox and it isn't occluded, they will generally hit the unit. If it's outside of the unit's hitbox, they will basically always miss, no matter how many times you play the shot over. The only way to fix it is to fire from a different position, as the way the soldier chooses their target area seems to be based on the position of the target tile relative to the position of the one who is firing. It applies to aliens shooting at you as well--it's very possible to be in a place from which a given alien can't hit you.
When the shot does not intersect with this small target area, it chooses a nearly random trajectory whose angle tends to go wider the lower the shot's effective accuracy. It's more likely to go near the target than it is to go wide, but not by a very big margin. On low accuracy shots (~25 or less), it is possible for the shot to go further than 45º from the target. On high accuracy shots (~75 or more), a straying shot usually won't go more than about 15º from the target, but that's still more than far enough to miss with only 1 tile separation between the shooter and the target unit. Large targets (cyberdiscs, reapers, sectopods), using vanilla hitboxes, the hitboxes are vastly larger than with small units. Because of this, your actual hit rate at shorter ranges (approx. 3-10 tiles distance) varies greatly by target size. For a small unit, hit rate is roughly identical to the rate that the target area is intersected, provided that area is inside the unit's hitbox. For a large unit, stray shots frequently if not usually still hit.
Compared to real life shooting, the X-Com units have abysmal accuracy. But also in real life, chance to hit a target varies greatly by the target's movement. Headshotting a non-moving snakeman at 30 yards with iron sights is a trivial task for a rookie shooter, but trying to hit a snakeman rapidly weaving side to side at 30 yards is very difficult without significant marksmanship training.
Technically speaking, the shot accuracy is not a percent chance to hit. But the actual % chance to hit (the target area) is so similar to the shot accuracy value at most accuracies that it is an effective shorthand to keep in mind either when firing or when explaining shooting strategies. The primary discrepancies are positioning of the target area relative to the target's hitbox (which varies depending on relative position of the target), and hitboxes not matching their sprites.
