I am have made a scene using POPs and an ocean surface simulating water runoff on a rocks. I can get the particles to render with the rock, but when I include the ocean surface with the ocean shader, the particles no longer render. I know that I would render the particles in a seperate pass and comp it in post later, but can anyone see why they will not render correctly like they are now?

Also, what do people suggest as the nest way to render the particles in this instance? I would also like to have them become more transparent with age.

I have marked the nodes where i have merged the objects to render together in red

Merging different objects together to render them inside a single object node is often bad for performance and causes the problems you are mentioning.
When you merge objects with different attributes they are often not initialized properly and are therefore not rendered properly.

The best way to approach this is to separate your major elements in different OBJ nodes. You can use the “object merge” SOP to bring in geometry from other OBJ nodes so you can organize them a bit better.