Even when unlagged was still common on servers in Europe, phenomena like the one you described happened to just about everybody, with pings in the 20-100 range. It's not just the shotgun, and unfortunately, not about 'clear hits' either. It was quite common (from my experience) to see players hitting dretches with MDs way, way off their hitbox (you could actually see the little green splash of blood appearing in thin air), behind corners, etc. Same goes for aliens hitting humans where they used to be (as opposed to where they actually are at the time of hit calculation), which is the reason why unlagged renders human dodging next to useless.
Another issue related to this is the apparent increase in alien range. Whether you were playing alien or human, you could clearly see that alien range is somehow 'augmented' past its non-unlagged norm. I believe this is not because of any actual modification to alien range, but rather a functional modification caused by questionable unlagged mechanics. Just imagine a situation where the human is backpedalling away from you, when you decide to attack. Just like in the example above, your position is not rolled back, but the opponent's position IS. Which means that the 'effective' distance between you and your target decreases, at least as far as unlagged code sees it. This might put your target within your range, very much in the same way as it put your target within the arc of your attack when he was dodging sideways.
Another problem with unlagged is, whether it actually benefits every player equally, regardless of that player's latency. If that's the case, the low-pingers' advantage over high-pingers is still retained, which doesn't make unlagged exactly helpful to what I would consider the target group of players - the ones with high enough latencies to make the game unplayable. Some time ago, there were a few attempts at making a latency-dependent modification of unlagged in Tremulous...
As for the aimbot question: what you're looking for is a simple horizontal offset setting, which can be readily changed. The aimbot's tracking still works normally, hence this could hardly make an aimbotter less likely to spot. You could make this setting (as well as the vertical one) random with every shot, but that would make the aimbot useless, plus it would certainly look very weird.