To turn off a layer you really want to mark it as non-printing in the file, ad that means the file needs to be opened and edited. It might be scriptable to speed it up, but my guess is that would take longer to write than it would to just open the files.
Are you saying you have 136 INDD files associated and synced within a single INDD book?
I don't know of a way to turn off a layer across all the files in one shot, but here's a possible workaround:
If you set up your files to use "Master Pages", then you could place those elements that need to be hidden/removed before pdf printing onto a layer within your master pages (in the file that is set to be the Style Source).
Yes, you will still need to go thru each file one time to remove the elements from the numbered pages, but then you will never have to do anything like that again.
I use "syncronized style-sourced Master Page elements" all the time to ensure I have consistent footers, slugs all the time, and I have also been tasked with making global revisions across multiple files, so this is my solution:
1. remove/change the Master Page elements on the Style source file
2. Re-sync all your files (master pages will be updated across the range of file).
3. Export your PDFs from the Book palette menu.
4. To make this even easier, I would suggest setting up a spare "Master Page set" (eg. called "B. with Logos") within the style source file so that it's quick to copy and paste the elements back onto the main Master Pages that are being used in your document files.
Hope this might solve your issue.