Engine noise.
 

Can engine noise cause any damage to audio equipments? crossovers? amp? pre out on radio?

can extremely frequencies be caused by engine noise?

Yes! Your ears.

If its just noise then you should be fine. But make sure all your grounds are good.

Never just use the oem ground wire for your deck, make sure its grounded to the frame of your car so its at the same ground potential as your amp. If there is any difference between the two that voltage will be on your rca cables and then amplified by your amps.