I'm not sure what you are talking about. If you put 100 comps in a single AE project and add them all to the Render Cue you can go away and let them all render. If you put 10 comps in an AE project and put all of them in the render cue then you will have to come back to the machine when they are done and open the next project. The only time 100 comps in a single project may cause problems is if the project file and cache starts stressing your system storage and memory capabilities.
I'm not talking about rendering them in after effects, I'm talking about starting an aerender.exe process, 1 single process rendering 100 or 10 processes concurrently rendering 10 comps. My gut tells me there would be little difference (or the 10 processes would be slower due to overhead) but just wondering as my gut is sometimes wrong