Components to avoid using on an ultrasonic cleaner
In case someone would wonder the same question. Here are some answers from the manufacturers:

Crystals (very clear and nicely explained):


  XTALs are generally sensitive for ultrasonic cleaning, as their
  function principle is based on a electro-mechanical oscillation.
  
  Ultrasonic cleaning on the other hand is vibrating the XTAL and thus
  might mechanically excite the XTAL in a resonance frequency and thus
  cause some mechanical damage.
  
  This risk is esp. high on kHz XTALs as they are based on a tuning fork
  crystal chip with a main oscillation frequency of 32.768kHz. There are
  however as well other “side” resonance frequencies in the system which
  might cause some problems.
  
  So there is the general recommendation to avoid esp. kHz XTAL to be
  exposed to Ultrasonic cleaning. MHz XTALs like the TSX-3225 are far
  less sensitive (as well because their nominal resonance frequency is
  far higher than the Ultrasonic cleaning frequency).


Transformers:


  the transformer is a little sensitive to the ultrasonic cleaning
  process since the transformer is not hermetically sealed.
  
  Questions arise when it comes to coils that are not hermetically
  sealed and run through a wash process. Approximately half of all
  non-hermetically sealed coils in the industry are water-washed during
  the PCB cleaning process and the other half are washed with an alcohol
  based cleaner. Of the ones washed in water it is quite rare for any of
  them to exhibit problems during their life cycle. However in some case
  transformers in the industry have exhibited shorted turns and opens
  later in the life cycle which can be attributed to the water wash
  process.


MLCC: (Yageo)


  To prevent the adhesion of the terminal electrodes being degraded,
  ensure that the ultrasonic energy  is not too high and follow the
  recommendations below:
  - cleaning time should not be greater than 3 minutes
  - frequency: 40 kHz


Film resistor: (vishay)


  Ultrasonic cleaning should be done with power regulated equipment.
  Older 25 kHz, unregulated equipment can damage joints and components


One IC manufacturer refers IEC 61760-1:2003-12 (surface mounting technology - Part 1: Standardized method for the Specification of surface -mounted devices (SMD).

Washing Process with Ultrasound &lt;= 80ºC / &lt;=6 min, Medium (Water, Ethanol, Isopropanol, Alkoxyde, Propanole, Aminoalcohol as well mixtures of the former).

For the rest, I didn't get any clear answers. I guess nobody wants to take any responsibility in case anything goes wrong with their products. They all recommend to test it by myself and take the responsibility. 

I can do tests on some samples. However, even if no components are damaged after the test, it will be a question if the process effected the component's long term stability/life time, etc. 

It is my impression that I shouldn't use ultrasonic cleaner at all unless it is a hobby circuit,