Your logo isn't showing in the PDF copy of the Quote because there is an issue with the image that you've uploaded in Settings > Company Information. The image issue could be due to file size (too big) or format (wrong format).
Resize and re-upload your logo image. Keep the shorter side of the logo image to 300px, and try compressing the logo image to reduce its file size. Also make sure your logo is RGB (instead of CMYK) and saved as a JPG or PNG.
Alternatively, you can also use the Print button to create a PDF, instead of using the "Save as PDF" button. Doing so would cause your browser to generate a PDF from the screen, and your logo would also appear if it's already visible in your account or Client Portal.