Hi Stephanie, in your capture of the EPS in Illustrator, you are showing the AI Color Picker with the color edited to Hex #99cc00. If you use the Color panel instead, it will give you the selection’s actual CMYK values, not the color managed versions of #99cc00, which is what the Color Picker does with hex values—hex colors are RGB.
Here you can see the Color panel is giving me the 40|0|100|0 CMYK value you are expecting. The top swatch in the Color Picker is showing the appearance of #99cc00 as sRGB—sRGB is set as my Illustrator working RGB space:

Th Color Picker opened with the rectangle selected and no adjustment. The #afca00 Hex value is the color managed conversion from the document’s assigned CMYK space into Illustrator’s Color Settings Working RGB space:
