Some things you do in compositions bloat the file size and can slow things down. Warp Stabilize is just one of them. There is also the chance that one of the comps in a project could become corrupted or fouled up in some way. Consolidating all of the AE work for a client in a single AEP does not sound like a good idea at all.
I have developed a standard file structure and naming convention that I have used for more than 40 years. It started out as file folders and paper documents matched to boxes of 16 and 35 mm film in racks with Client>Project Name>Film Name>Scene and even Shot numbers. Many of my projects have standard libraries in them for assets that include everything from AE templates to sound effects, music stingers, and narration. Basically anything that I can use again in another project goes in a library folder that is separated into categories. The most important part of this system is the log. It started out as a paper document with columns and descriptions. It is now a spreadsheet that I keep for every client. The format fairly closely matches a standard film production call sheet. That's how you efficiently keep track of hundreds or even thousands of assets. A carefully thought out naming convention also helps you when you search your hard drive.
I would suggest that you grab a sheet of paper and a pencil and try and figure out the best way to organize your clients, your footage, your projects, and every other asset that you usually use in a project and then get in the habit of organizing those folders and files in a standard way so you can go back three years from now and find that really cool text animation you created for episode 1 with just a few clicks of a mouse.
Putting 100 compositions for a client in a single AE project will keep the projects together but you won't be able to search for anything specific unless you open the project. Unless you develop a footage and composition naming convention that is standard for every project you'll never find that really cool animated bar chart that you created 9 months ago if it is buried in a AEP with 100 comps.
Personally I create an AE project for each scene in a script that requires shots that can only be done in AE. I almost never edit in AE and if I do the edited sequence is usually only long enough to cover a sentence or a phrase of music. If I'm going to assemble these sequences into and edited piece most of the time I render the footage and do the final edit in Premiere Pro. Occasionally I will nest a few comps in a master comp and edit and render the sequence that way.
One more thing. Anything that you expect to use over and over should be saved as a AET, After Effects Template, so you never loose the original. The option to do so is at the bottom of the Save panel where it says File Format. You just have to select it as an option. You can also create a template by doing a save as.
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