Can't say as I particularly agree with either answer.
Judo is primarily a sport, which has some self-defense applicability. Some schools emphasize the sporting aspect, but many still teach the self-defense applications of escapes, come-alongs, and so forth. At the upper level of instruction (think, years) there is some striking and even weapon work, primarily the hanbo (short staff) for police work.
Limitations are that there is almost no striking taught and grappling is very limited in self-defense... What do you do if there is more than one attacker?
Hapkido is, I agree, rather rare and finding a good instructor might be difficult. But it's a put-together style that includes striking, a limited amount of grappling, and some weapon work as well. They have some nice cane sets that translate well to almost any improvised weapon.
If you want to see Hapkido in a movie-fu situation look up the incredibly cheesy old "Billy Jack" films. Tom Laughlin's instructor was a prominent Hapkido guy and they even put him in the second film.
At what stage of learning? At the beginning there are many cons in a fight due to the fact that you don't know so much. The cons become less as you train hard and learn more. For a master there are much less cons that there will be for you and someone really really good will have no cons at all and will be able to deal with just about any situation. In essence your question is which art is better even though you worded it differently. But the answer is there is no better art. The art is a toolbox and it depends on each and every practitioner how well they know how and when to use the tools.
Can't decide which one to pick? You pick the one with the better teacher. One teacher is bound to be better than the other. Still can't decide which is the better teacher? Ask for free trial classes and try both of them out. Picking the best teacher is very important because that too will determine how good you will be. If the students in the school don't know what they are doing neither will you.
I don't see any cons to either. There is only pro for both.
Both cyou can learn a lot. It really depends on 2 things in my opinion.
1 What are your goals?
2 Finding a good instructor
Most judo schools that I have seen today focus on judo as a sport instead of judo as a martial arts (self defense).
But there are some great instructors that do teach judo as a martial arts and students can still compete in the sport side of judo. Everything starts with having a good instructor. Whether your goal is to compete in a sport or to learns self defense you need a good instrcutor. If the instructor is not ood then you will be limited because you won;t learn things that you should.
Judo's pro is that it is a fantastic grapling and throwing art. The con is that you don't really learn striking.
Hapkido's pro is that it is pretty rare. The con is that it does exist and it sucks.
Grappling arts like Judo are the best foundation for a fighter.
I'm deciding which one to do.