Sounds like a cool setting. I second Cyberpirates! for resources. I think there are also some nautical based resources in
Target:Smuggler's Haven IIRC and
California Free State might have some coastal pirate type info, but not much -- man! I'll have to dig out my copy and look, you have me curious now.
Oh, yeah and I think
Hazard Pay has an Ocean section; I haven't seen that one though.
Other ideas for your players or runs:
* Guard a sea-based shipment for 'XYZ' corporation from 'ABC' corporation
* Explore underwater ruins
* Capture live specimens of <insert para-critter>
* Toxic sea shamans/spirits
* Underwater corporate research stations or hit an
Arkoblock* Hit and run campaign - have an over reaching goal, or just go full on Pirate!

* Map underwater location or provide support for science team doing the mapping
* Underwater Casinos! Need I say more?
I personally would want a rigged out submarine, but that may just be me. And a peg leg --- with a panther assault cannon mod of course...

OOhhh...or a grappling gun cyber-arm!