It is not a good idea to take x-rays after a cleaning (D1110) for the fact you just stated above. If a patient has moderate to severe plaque/claculus you want it visible on the x-ray. In order to bill root planning/scaling D4341/D4342 you need to the following;
1. Indications of moderate to severe calculus
2. Presence of periodontal disease
3. Part of a pre-surgical procedure or to prevent surgery
Most offices will take x-rays, then cleaning, then exam.