Harg... no, shivan ships are definitively not organic...Damn derelict lol
Have you ever seen an organic creature with sensors and turrets, with beams?
Ok, more seriously, an organic creature wouldn't be affected by disruption weaponary, it would bleed when hit, something like that,and the shivan would have the same kind of weapons, olny smaller, not those plasma launchers.
Plus look at the ships... do they look organic? That's metal, for sure.
Volition did thought about the shivan ships as organic ships (look at the apocalypse concept pic, it's obvious), but it's also clear they trashed the idea. Vasudian ships are probably more close of the organic ship (look at the strange green "veins" on the anubis, if you don't believe me...)
For the vacuum stuff in the shivan ship (hall fight cutscene)... That's not vacuum. Put a terran in space vacuum without spacesuit to see what happens ( summary: it freezes in half a secon).
For the shivans breathing nebulaes... Damn, don't you think they have enough nebulaes in the universe not to blow Capella to have one more? lol
Well, after all, you know what I think
(look above if not )