Actually there is a pretty simple way.
1. Import all your original clips, preferably put them in a folder in AE project, helps keep organized.
2. Select them all and drag to the “create new comp” at the bottom of the project window.
3. In the dialog that appears, select “multiple compositions”
4. This method creates a comp for each of your clips with it’s exact file name
5. Now it’s just hard work, open each one of the compositions and paste the effect you want to the clip inside.
TIP: First, cmnd-C the effect from the “effect control” window. Now, select every COMP in your project, hit the numpad enter to open them all or double click one of the selected comps, and repeat this sequence:
cmnd-A (select all layers, in your case, just one), cmnd-V (paste the effect) and cmnd-W (close the comp window and move to the next)
That should at least make it go faster.
6. Render queue. Done. Just remember that the files will have the same name as the original, don’t export to the same location