CT scans will emmit more radiation than the regular xrays, and some contrasts could be harmful to the foetus, some contrasts are radioactive (but not nessarrily used for CTs, but other medical immaging), so that could be an issue re: conception as it might take some time for your body to eliminate it.
The contrast used for CTs are generally iodine based, so if you are allergic to iodine, iodated dye or shellfish, you might have an allergic reaction.

If the kidney cyst is more sinister, pregnancy hormones could stimulate its growth leading to a more complicated situation later on.

I would be inclined to trust your doctor, and get scanned on CD1, if you don't get PG. If you do get PG you might just need the cyst monitoring during the pregnancy, then deal with any further problems as they arise.

I hope this has help a little.