Note: I never tried data merge within a PDF with an Excel file but found some info about it.
Apparently it might be possible to do this with Adobe Acrobat Pro. You can create forms with fields using Acrobat Pro and there's an "import data" functionality.
You'll create some fields in Acrobat Pro and link them to the same cell names of an Excel sheet; that should auto-fill them and logically when the Excel file will be updated, the fields will be updated too.
Fields can be transparent and you can apply them anywhere on your original PDF exported from Indesign. One thing though, your client will need Adobe Acrobat Pro (not the Acrobat Reader) to save their data in the fields, and you'll also need to provide them the fonts or use the safe fonts.
I guess 5000 items should work, that's certainly going to be a lot of work to set up for you. In worse case, if your reps computers or the software can't manage that many data, the catalog might need to be split in sections and reassembled within Acrobat once all the data are filled in each section.
One thing that might be annoying is when you'll make updates on your Indesign file and re-export the PDF, I'm not sure you can quickly re-apply all the fields. You might need to copy/paste them from one PDF to the other or re-do them all again. That's something maybe the new Acrobat Pro fixed and made more convenient.
I found this link about it:
More links here:
Illustrator invoice to client useable PDF
You can create forms from Indesign and export your PDF as interactive. And then use the import data to link your Excel, and fix the fields if necessary.
Apparently it can be a bit buggy if you use libraries but it's probably faster to create at least the fields in Indesign.
Basic design layout considerations
The auto field detection process looks for certain basic form design
elements. To help improve the process, here are some general tips to
consider when authoring a form.
Keep it simple and uncluttered—use ample white space or separator lines between areas.
Keep your layout well-organized so the field tab order is set properly.
Keep text within a 10–24-point size range.
Avoid drop shadows or ornate graphics on text labels.
Avoid overlapping fields, especially within areas that use underlines.
Avoid heavy decorative graphics or transparency on the page.
Use white as the primary background color; avoid putting text on top of colored rectangles.
Use the same style for each type of form object.
Do not use the same text label across multiple fields.
Make sure custom fonts use the proper encodings. In Acrobat 9 Pro or Acrobat 9 Pro Extended, you can use the Preflight tool to