Does water damage a fiber optic / cat5 cable

The real danger is at the terminations, where corrosion can start. As for the cables themselves, they're fine in water, although I'd be careful using it in a corrosive solution. Keep an eye open and you should see plenty of examples of network cables, including fibre, used outdoors in the weather. I know of examples where cables sit permanently in water and have done so for many years. Network cabling is no different to any other kind of electric cabling. Keep the ends dry and the rest doesn't matter.

Replacing the bundles would be expensive. If you've got it in your budget (or insurance will pay for it), do it.

As long as there were no nicks in the PVC sheathing, you should be alright (http://www.cat-5-cable-company.com/faq-bury-burial-cat-5-cable.html).

It's hard to tell if you had any nicks in the plastic, but I imagine that you're going to find out. Do you have any spare cables in the bundles? I would save yourself the time of panicking during an emergency and find and label them now. Create documentation on how to replace a poorly performing cable with a spare.

Know that if you don't rerun the cables, this event is going to be the scape-goat for all future network performance issues forever, until more cables are run.

I don't think the water will have any immediate effect as long as the water never entered the cables--obviously copper wiring will oxidize if given the chance.

My argument for re-running the cable would partly be that you can't reasonably ensure the current cable will dry instead of growing mold/mildew and turning into a slimy nasty mess.