For PVE there is alot of information floating around. Some people suggest stacking HP as high as possible (there is a VG on my server with 29.x K HP). Is it true some boss fights do only yellow damage and therefore shield / absorb are useless?
Yes, some fights do make shield/absorb useless. This is much more prevalent in TfB.
Is it worth building just for these boss fights or will it have a negative impact on the rest of my abilities?
You are definitively having a negative impact on the rest of your stats by building for endurance. Deciding how much of that impact you want to have is up to you.
Is there a CD on shielding abilities, or is it every attack has a chance?
Shielding, and defense as well, are always available, but can only occur on ranged/melee attacks.
Finally I was really hoping to get a link to some full tank spec tree and see exactly what people have been ignoring for the sake of extra def / endurance, or if they have at all.
Higher Damage/Threat Build:
Higher Hp Build: