Nearly all German/Ironblood ships were initially only available during events (until later updates added the War Archives and modified the build pools). However, those that were always available full-time almost all have some justification to being more readily available to Azur Lane.
The Königsberg-class and Leipzig-class light cruisers were built by the Weimar Republic for the Reichsmarine, and thus predate Nazi Germany (or in-universe, the formation of the Siren-tech using Crimson Axis). This is also reflected in their outfits having darker shades of red and their riggings being far less animalistic than those of later cruisers whose real-life counterparts were built under Nazi rule.
Prinz Eugen is well-known for having survived the war and being taken as a war prize by the United States; since the US's counterpart, the Eagle Union, is part of Azur Lane, it makes sense that Azur Lane would have relatively easy access to her.
Z23 didn't survive the war, but was refloated by the French, who then used her for spare parts and eventually scrapped her, giving a good reason for her to be available to Azur Lane forces.
Roon and Friedrich der Große don't have any basis in real ships and are being made by an Azur Lane-led R&D project.
The only exceptions are Graf Spee and U-81, who don't really have any clear basis for being available to Azur Lane forces on a regular basis.
Why is a shipgirl's affection raised by sending them into battle? It's a sign that the Commander put their trust in said shipgirl that they can win the battle. Shipgirls initially were created as weapons, and you gain their appreciation by putting them to good use. Overdoing this, and this will no longer hold true, becoming some form of slavery instead.
The more they love the Commander, the better they perform in battle. Love is a real thing in real life, it motivates you and makes your perform better. It can also be said that love is a sign that they begin to turn into a human, not just a emotionless weapon (Gascogne perhaps exemplifies this more clearly than anyone else).
Enterprise's(Anime) choice to use her planes as mounts is due to wanting to compensate her limited anti-air abilities, something her sister, Yorktown also had and got severely injured by enemy planes.
Akagi and Kaga being manipulated by the Sirens is similar to how Eve was tricked by the serpent. To hammer that analogy further, the Orochi resembles a snake.
Monarch is a redhead- i.e., the almost literal Redheaded Stepchild of the King George V-class.
In her character quest, Akagi hangs out and drinks together with Graf Zeppelin. While this may seem like a regular random interaction between the two factions' carriers, those who understand both ships' histories will feel more like they are having a more sisterly encounter; Zeppelin's primary design is based on an improved version of Akagi, making them look like sisters in spirit.
Considering how the Commander was revealed to be the one with the highest affinity to Wisdom Cubes, it makes sense that the shipgirls (who are formed via those) have a natural attraction to you. The Northern Union girls know this fact better than anyone else from the other factions, but natural attraction by itself doesn't do much else. If you purposely do nothing with them, your relationships with them will not grow; at best they will stay at "She wants to know you better" (written on their marriage certificates at Stranger level), and as mentioned before, your girls won't be able to fight with their maximum strength. After all, your girls are still girls at heart, and meaningful gestures are needed to make your girls fall for you (yes, just like how you would try to court a girl in real life, but harder): understanding their feelings, hobbies, shortcomings and such, and finding appropriate ways to deal with them (read: sending them to battle to signify that you trust them and make them more open to you), for example, sympathizing with Enterprise's ordeals and promising to be with her always, and so on. You may have a good headstart by piquing the girls' curiosity (via your innate affinity to Wisdom Cubes), but if you don't make use of your advantage you simply would not progress any further.
The ranks of Exercise Mode use a combination of naval ranks and army ranks. Paired with the fact that the Commander is an Eagle Union naval officer, this may reflect the New York Port of Embarkation, which not only was the single biggest military port system in America during WW2 but also was mostly utilized by the Army.
The main story line is the echo that Shinano speaks of that has been set up by the sirens. The events are where we are in the time line.
Type II shipgirls note Starting with Yorktown II, Hornet II, Langley II, Hammann II, and Northampton II inherit the appearance and memories of the original shipgirls with the same name. Considering how the USN renamed a number of ships from newer classes mid-construction to honor the service of the preceding ships lost during the war, it is like a reflection of this behavior - passing the name down to keep the ship's image alive and continue adding to its history.
This also explains why none of the "Parallel Superimposition" shipgirls were added as Retrofits. They would have to be their original class and Type II rigging represents a ship class change rather than a hull refit or conversion.
Why is Observer Zero's rigging based off of a jellyfish? The bell of the jellyfish strongly resembles that of the Turritopsis dohrnii, better known as the 'immortal jellyfish,' which is famous for its never-ending cycle of death and rebirth, mirroring her purpose in resetting the timelines in Dr. Aoste's master plan to force humanity to evolve.
Most destroyers are young mid-teen girls like the four starters, but there are some who are as young as kindergarten kids like the Mutsuki-class destroyers. Why field them in battle, despite knowing that you are using Child Soldiers? It is because of desperation: as stated after the opening scene, humanity is waging a losing war against the Sirens, and they need every able body to take up the fight. This could be handwaved by the fact that even small destroyer kids are special ones with riggings, but using them in battle is not meant to be a comforting thought.
G/Ash/Enterprise META stopped Ember/Takao META from outright murdering the Commander in Ashen Simulacrum. When asked why she did this, she’s at first evasive, only to become surprisingly meek and quiet when pressed, and then admit that it was because she couldn’t go through ‘that regret’ a second time. Think about that. Did the Commander in her timeline die, and she was powerless to stop it, leading her to become what she is now?
The recently revealed fate of John Archer (who captained the nuclear CVN-65 Enterprise, befriended her during her training, and sacrificed himself to destroy Pandora's Box) heavily implies that this was the regret that she didn't want to relive.
