01) Yes, both Punished "Venom" Snake and Big Boss were in a nine-year coma simultaneously. The latter was stuck within a legitimate state of unconsciousness whereas the
Medic/Venom Snake was placed under an artificial one by orders of Major Zero/Cipher to create the doppelganger ploy. He wasn't allowed to awaken until the real Big Boss surfaced back into the world.
02) There appears to be an almost unanimous praise for the "Truth Tapes," especially Major Zero's voice actor whose sole appearance is exclusive to the cassettes. However, some scenarios found in them feel more like a "literary device" meant to provide the listeners with a seemingly significant encounter that logically wouldn't have been recorded in such a convenient manner. There aren't many notable revelations to the best of my knowledge. They explore the downfall of Zero/Cipher through his relationship with Paz and Skull Face along with his flitting effort to assist Big Boss in his "final" moments prior to succumbing to his parasitic infection. Anyway, it's possibly the last piece of
Metal Gear mythos we'll ever receive so enjoy them!
03) It isn't implied. Huey Emmerich and Dr. Strangelove shared a relationship that lead to the birth of Hal/"Otacon" while developing the Sahelanthropus project for Skull Face. Stangelove eventually realized that Huey had planned to utilize their own child as an experimental pilot for the bipedal mech and she retaliated by placed Hal into protective custody in the United States. Sometime afterward, Strangelove accidentally locks herself inside the Mammal Pod and Huey willingly allows her to suffocate in an effort to remove her as an obstacle in how he ran the Metal Gear enterprise. His implications that Skull Face killer her and, later, Strangelove intentionally committed suicide were plain lies to hide his guilt. The truth of this matter is pretty much revealed in her confession tape following Huey's exile from Mother Base.
04) Sadly, it's a plot point that goes unresolved in the final product much like Eli/Liquid Snake possessing a vial of the English vocal cord parasites. The collector's disc for
Phantom Pain reveals that there was supposed to be another chapter to bookend the entire narrative, "
Episode 51: Kingdom of the Flies." It would've explored Venom Snake hunting down Eli, Sahelanthropus, and the extracted child soldiers on an isolated island off the coast of Africa. A final showdown ensues, reminiscent of battling Paz and Metal Gear ZEKE from
Peace Walker. Ultimately, Snake and Diamond Dogs would manage to put down the latest Metal Gear before discovering that Eli had infected himself with parasites in an attempt to kill off any adults that he would meet following his escape. The mercenaries decide to leave him behind as a result, air-lifting what remains of ST-84 Metal Gear out of his grasp. Venom orders an attack on the island to ensure that any potential remnants of the parasites are burnt off the face of the earth. Before that could take place, Psycho Mantis appears before Eli to use his psychogenic powers to remove the organisms out of the child and they move themselves to safety. Yup!