If you notice the same rendering lag in the Files app or macOS Preview, this is unfortunately not in GoodNotes' control because the app uses iOS PDF rendering engine.
Reducing its file size (macOS only)
Try opening the PDF in macOS Preview and clicking File > Export..., selecting "Reduce File Size" under "Quartz Filter" and importing the result PDF to see if the slow rendering improves.
Compressing the PDF
If you don't have a Mac, compress the PDF with an online tool, using the highest compression if possible, and try importing the result PDF.
Resizing the source document
Better yet, if you have access to the source Keynote file, please try the following:
1. Open the file in Keynote and click the File menu > Reduce File Size... > Reduce a Copy.
2. Open the reduced Keynote file, click Document in the right sidebar and resize the page size to Letter or smaller:
3. Click File > Export To > PDF... > Next... > Export.
4. Import the result PDF to see if the rendering improves.