You forgot the most obvious link: in many mythologies, a ferry is used to bring the souls of the dead to 'the other side'.
There's no doubt that the Shadow Temple possesses a strong link with Death. However, I think jumping from that to 'Bongo Bongo was a necromancer' is a little bit of a stretch. It seemed to be fairly self-evident in my eyes that Bongo Bongo was the embodiment of all the negative emotion that had accumulated in Hyrule's bloody history.

__________________
My Timeline Theory

Zeldas completed:
LoZ, AoL, ALttP, LA(DX), KnS, OoT, MM, OoS, OoA, TWW, FS(only on Silver Keys), FSA, TMC, TP(Wii), PH.
MAN I love the Zelda series.