Though alot has been fixed, more bugs and desync still occur. The USN and UK harbor both have tiles behind the harbor that cause the defenders to crash. Leaving the attackers to take the harbor with minimal crashes.
The crazy part is there isn't a form of punishment nor has SDE done anything to remove this glitch. Instead of blocking off the room from being accessed they continue to allow it. Last week UK was taken using this glitch.
Every harbor has a glitch of some sort. I know that KM would lock up in a battle state but no battle would actually be happening.
But again it's a rare chance. If it happens, it happens hard.
As to your other questions.
The importance of your current ship doesn't matter to most fleets. Being in a low level ship has its own uses in ocean and harbor tile rooms. Each fleet has a idea that you could follow and help. Even in a cruiser, all the way down to a frigate. In Knights templar we have a player who plays in a cruiser in the HT. In some cases he is able to sneak in and kill Bb6s. I think his kill count is 8-10.
APA serve no purpose in ocean tiles. The ship can still be used as a ship but it wont capture the room. In the harbor tile a apa can launch landing forces onto the harbor.