From what I know of Hapkido and Aikido, they have very similar mechanics, but not "practice" systems. Hapkido seems to either be a "grab my wrist" or "fight" scenario, while Aikido is more of a "partnered" (i.e. balanced) approach to training.
Both use the same dynamics of throwing, takedowns, and pinning, but I think the Hapkido folks are a little "shorter" with their techniques than the Aikido ones. Short-cutting the techniques makes them extremely painful, but doesn't allow the uke a chance to protect himself very much, and while they have similar dynamics, I would suspect that Hapkido would incur more training injuries because of that... JMO
Hapkido is more of a blend of TKD and Aikido and the "angular" techniques of karate based skills is usually sharper than those of throwing based techniques because part of the training is to help the uke learn to protect themselves with ukemi as well as to teach the nage to throw or pin. Hapkido gives such little consideration to that side of the equation, I suspect that you "do what you can" and hope for the best... but both arts can be brutal at the level I'm accustomed to playing.