I noticed a few odd things today.

[PvK]

#1 sounds like a bug, though since "shields" are fantasy tech, having a thin shield bubble left after generators are destroyed could be a reasonable effect.

#2 I don't think your work-around would work easily, because it is possible to capture enemy ships. However there are ways to program around it, but MM might have better things to fix...
Why don't you just alter your ship name slightly, like adding a "." or a "2" or something?