Your getting bad results due to light refraction from your material. What you think you're measuring isn't going to be properly reflected back to you through your material. I've tested subsurface glass/acrylic of various thickness and accuracy is directly proportional to thickness. So as previous poster mentioned, if you must profile this way, use as thin of material as possible. Most likely you will find your swatches are measuring much darker than actuality.
Are you using any white ink behind colors? My most accurate acrylic profile is from measuring with heavy white ink directly on surface of any material.
If you are not using white ink, a transmissive spectro could be useful (probably not worth it). You will want to use a higher ink limit since your colors are not going to be reflected very well without white ink. Your spectro isn't just measuring through the acrylic to the inks but also, since inks are translucent, whatever is under the ink. If it's a white piece of
paper, then your are effectively making a reflective profile.