Either way will work, but pre-rendering them will probably decrease the final overall render time some. The problem with pre-rendering(if render times are an issue) is that if the client changes his mind, you have wasted time rendering something you won't need.
I have a very fast computer, so my workflow(if doing the entire thing in AE) would be to set up my master comp with the icons as precomps and render the entire thing at once. If the client wanted to make a change, I would only need to change a precomp and be done. Alternatively, you could just set up each icon to render out with an alpha over night, and then you have everything and it will be pretty quick to make changes and renders to your file...
Sorry if it's not much help, there just really isn't a right or wrong here, other than what will be the most efficient workflow for you and your computer system.
Johnny Cuevas, Editor
"I have not failed 700 times. I have succeeded in proving that those 700 ways will not work. When I have eliminated the ways that will not work, I will find the way that will work."
---THOMAS EDISON on inventing the light bulb.