We've fixed some issues in last beta http://beta.plantuml.net/plantuml.jar
There is a not-very-documented syntax for FontColor that allow to automatically switch between two colors depending on the backgroud. We've just extended this for HyperLinkColor so you can now have:

@startuml
!$FGCOLOR = "black"
!$BGCOLOR = "white"
!$DARK_BG = "#565656"
<style>
root {
BackgroundColor $BGCOLOR
FontColor #?black:white
HyperLinkColor #?blue:cyan
LineColor black
}
note {
BackgroundColor $DARK_BG
LineColor red
}
</style>
rectangle "Link to [[google.com Google]]"
note bottom
And here's a long description about something
that may or may not include a [[google.com cool link somewhere]]
endnote
@enduml
Does it help ?