Cheerfull,
The test that you had when you were pregnant may have just been a screening to check for markers, not the genes themselves. So yes it is possible that your son has CF -- with your daughter's diagnosis he should be checked again with full genetic testing. It may be cheaper if you already know your daughters genes so they know which two to look for -- you can email the ambry guy on this site and ask him for sure, I could be mistaken about that part.
How was your son tested for celiac? I know there is a blood test that is 85% accurate, but I was told to be sure the best test is the colonoscopy to get the biopsy done, which is very accurate. My daughter was tested (with both blood test and biopsy) for celiac. She does not have it but she does still follow the celiac diet because she feels better without eating wheat.
Also, assuming your doctor is correct, and your son does for sure have celiac, it is not out of the realm of possibility to have BOTH CF and celiac. Both diseases are genetic from the same region (European) I don't have the statistics at my fingertips but I know I have read that those with CF are at a greater risk for having celiac (statistically speaking)