Scientists may have religious beliefs, but that does not make the beliefs scientific. Just because a nuclear physicist or someone at ISRO believes that crushing lemons or breaking coconuts makes a flight safer (or whatever it is supposed to do), does not make it a scientific truth.
No one claimed that they are scientific truth. So your entire argument based on that premise become redundant.
It's just an age old practise in Indian culture and there is nothing obscene if they are done. It just gives a subconscious belief and confidence which keep the scientists in high spirits and relaxed which are crucial.