Hi Arnold
If all you have is a PDF, which I presume you have placed into an Indesign file, then if you also use Illustrator I would try this first:
– see if the PDF has been created using Adobe compatibility settings by trying File > Open in Illustrator. If successful, ungroup/remove clipping paths etc until you are able to select all the objects that have the colour fills/strokes (or select the objects directly in the Layers panel). You can then copy the objects in Illustrator, paste them into an Indesign doc and Indesign will create all the swatches automatically.
If that doesn’t work, you can do this (this method works with placed files including images too):
– create a CC Library for the colours
– in the CC Library pane click the “+” icon at the bottom and select “Extract from image”. This opens Adobe Capture which lets you move the sampling circles to select up to 5 colours from the source. Strictly speaking, it’s creating a tool for creating themes but it will add the colour swatches to the CC Library.
– add the colours to your Swatch panel in the current document if that’s what you want.
– loop this process selecting different sample points if you have more than 5 colours to add. This isn’t solving the problem completely, but sounds a lot quicker than doing it with the dropper.
If you are the agency’s customer, I would probably expect them to provide an Indesign Library that you can import or give access to a Shared CC Library that you can copy swatches from.
Or if you can get a native indd file rather than PDF with the colour samples, e.g. as filled frames, then you select all the frames/objects and from the Swatches panel “Add Unnamed Colours” and it will add swatches for the fill and stroke colours in one go. This is an option when you are working with Illustrator too.
Nick