In 88 Flak, battleships/carriers (large capital as they are known in 88 Flak) are an essential part of any assault force. It doesn't really have much to do with actually carrying fighters anywhere, but for providing support for any fighters operating nearby. A large capital is a support ship. While it excels at taking down other capital ships, especially other large capitals, it is useless against anything smaller.
This creates an interesting dynamic whereas you can either leave the large capital on the fringe of battle to give fighters a place to land and re-arm, or you can bring them front and center to help take down the enemy's large capital which is supporting their own fighters. Once the large capital goes down, the fighters are on their own, and are out of support.
As for gameplay oddities. To my knowledge it all works very well. If the large capital you docked with dies/logs off/etc. You will respawn on the last base they docked with. So for example if you were in a fight, and docked with the large capital, you will respawn off that large capital when you die. If that large capital is destroyed/logs off, you then respawn at the base where they last docked.
The only thing I remember that would sometimes bug up was when a carrier goes to another system with another player in dock. 90% of the time this would work fine, and when you undock you simply are transported through the appropriate jumpgates and then undock from the parent ship as always. However it would occasionally bug up. This usually does not even happen in the first place though because most people don't stay docked on large capitals for any longer than needed to rearm and repair.