As David says, you can place the .ai file directly in InDesign. There’s no need to save as a PDF first, although it should make no difference to the outcome.
An InDesign document is always either CMYK or RGB, but what will actually output to PDF will be whatever is actually in the document. If there are spot colors, there will be spot plates. If there’s no CMYK, then the CMYK plates will be blank and you’ve nothing to worry about.
Before you panic, check a couple of things in InDesign:
– In the Swatches panel flyout menu, select Ink Manager and verify that the spot colors are there and that “All Spots to Process” is NOT checked.
– Now open the Separations Preview (Window > Output > Separations Preview). If you see your spot colors, click the CMYK eyeball to turn off those plates. The logo should remain visible. Turn on CMYK and click the eyeballs for the spot colors. Logo should disappear and only other non-Pantone items should be visible. If that’s the case, you can relax.
If you DON’T see the spot colors in InDesign, then they’re not there in the Illustrator file, no matter what Illustrator’s swatches panel tells you. A spot color can be a solid ink or it can be a CMYK formula (e.g., Pantone Bridge colors).
If a PMS solid color has been converted to CMYK, it will still appear as a spot color in the Illustrator swatches panel, and it will still have its original Pantone designation, but it won’t actually be a Pantone Solid ink. Double-click the swatch to reveal its true nature!