The OP asks about the "fairness" of two cases in Torah Law claiming that they seem "unfair":
A man who refuses to give his wife a get (divorce); for whatever reason.
A woman who never received a divorce from a husband who is still alive, but incapacitated, or his whereabouts and/or living status is unknown. (missing but we do not know if he is in fact dead)
In both cases, Torah law does not have any simple usual way to dissolve the marriage other than waiting until the husband willingly issues a get (bill of divorce). This unfortunately leaves the woman as an "agunah" or chained to a (seemingly) dead marriage.
Of course, the true depths of Hashem's wisdom on any matter is not known to me. However, I feel it is better to present what we do know, since the best partial answer is better than none at all IMHO. People will benefit from an answer that guides us to the proper conclusion for the most part, despite the limitations on human wisdom and understanding.
Lets start with #1.
First of all, the assumption that justice and fairness would dictate: "that a man who refuses to give a get is evil; or that any woman who claims she wants a divorce is certainly allowed to move on with her life", is absolutely wrong. Actually, common sense dictates that the only true justice in the matter is to simply wait until the husband wants to willingly grant a divorce.
Please consider, in any other transaction or relationship (besides marriage) between human beings in this world, agreements are considered binding by society. Secular law, which many of us look to as a first sign of the definition for common sense justice, has two laws available (in many countries; not just the USA) for those who break, or want to break, agreements.
a) Specific performance. This law allows a court to order someone breaking an agreement, to fulfill it anyway even if that party wishes to get on with their life without fulfilling the deal any longer.
b) Detrimental reliance. A person who breaks an agreement can be sued for heavy damages if the other party suffers by relying on their partner's word to fulfill a deal.
If two people agree to the sale of a house, and enter a binding mutual contract, we all know that "justice" assumes they must complete the deal, and anyone who breaks it (seller or buyer) is obviously in the wrong. We never say that the sudden wish of one party to back out and "move on with their life" is ever considered "fair" behavior. We have a word for such people: liars and cheaters.
This is almost always true even if the party backing out proves it has some new unforeseen loss at stake. The court says: Tough Luck. You promised. Your partner doesn't have to suffer because you have an issue.
The Torah describes the marriage bond/agreement in Genesis 2:24:
"Therefore, a man shall leave his father and his mother, and cleave to his wife, and they shall become one flesh."
Now undergoing surgery to willingly become "one flesh" with someone is a serious life changing move. Certainly, we understand that such an operation is probably permanent and any attempt at reversing it will be rare, and probably quite exceptional and painful.
If someone agrees to sell their home, and has received money etc., a secular court would demand that the seller fulfill transferring the deed!
So why would we think that a woman can simply tell a man after being married for some time, that she simply wishes out and it would be automatic justice to have the man grant it??!! That's ridiculous.
Since when does a man invest his life, money, and emotion, into a "one flesh" transformation, have children etc. only to be told that just because his partner (who promised to be his wife) is now changing her mind, that justice demands he simply accept it? Obviously just the opposite should be true. Justice would demand that no woman can simply dictate that her partner dissolve the status of "one flesh" because she is changing her mind. Who gave her the right to break the deal??!
Now you might say that if we can show the husband is abusing his wife, so that it is obvious she deserves to be released from her obligation to keep the deal, then the court can issue a divorce without him?
The simple answer here, is a verse in Koheles 3:15 "...V'HaElokim Y'vakesh es nirdaf" ("...and G-d seeks the pursued.") G-d himself finds out who is the pursuer and who is the pursued. Who is wrong and who is the true victim.
A marriage is such a complicated state, that it is impossible for fellow humans to be able to know what went on behind closed doors and decide who is right and wrong in a marriage. Only Hashem can do that. Also, they can both be guilty.
If so, there is no human court that can regularly dissolve a marriage between two people. They just do not know who is at fault and to what extent. They lack the ability to justly deprive a man or woman of their marital bond (especially if there are children involved).
Now the fact that one side's alleged abuse may be enough to grant a divorce is a safek (doubt of human judgment). The existence of a "one flesh mutual bond" between the man and wife is an undisputed fact. (vadai)
The Talmud throughout often says: "aino safek motzi midey vadai". "A doubt in judgment cannot remove the status of an undisputed fact."
Therefore, the courts are not empowered to touch the marriage directly. The husband must willingly issue the release.
2 What about a missing husband or one in a coma?
a) All of the above applies because we cannot deprive a man of his marriage since he may wake up from his coma today or he may walk in with a good excuse for being absent.
b) A Jewish woman by entering marriage is not just doing so for herself, but is becoming the guardian of the office of the Jewish married woman. It is a public status. She is responsible to uphold the sanctity of the institution of marriage, for the public, even at the price of her own suffering.
When a woman accepts a ring under the chuppah and becomes "mekudeshes to a man" she has willingly accepted that she may only have relations with that man only, for all time, until death or willing divorce occurs. If we were to be able to cancel marriages due to comas etc., we would cause such a weakening of the respect for marriage laws that courts would start tampering with just about any marriage; causing adultery to increase and marriage to become meaningless in society.
However, the Talmud does record that a husband may grant his wife a conditional divorce when faced with risk of his disappearance. For instance, all the soldiers of the house of King David would regularly issue conditional divorces to their wives, on the eve of war, in case they became MIA. That way, their wives would not become agunahs. (Ketubot 9b)
We see though, that for whatever reason, (perhaps because of the "weakening of the respect for marriage laws"- King David unfortunately was tempted by this very loophole with Batsheva; or simply because people do not feel emotionally good about writing conditional divorces) people just do not avail themselves of such insurance policies although they are halachically available.
Therefore, such chained women are no different than any other tragedy that we must rely on G-d to answer with our full faith.
This entire answer by no means could possibly cover every angle in such a short post. I am aware of other issues. However, this does serve as a firm core basis to approaching the issue of the justice and fairness of Jewish divorce law.