Dear Prashanth,
Taking a “head bath”, or a shower, is in itself nothing unspiritual. On the contrary, Yogananda quoted the Indian saying, “Cleanliness is next to Godliness,” which also meant physical cleanliness, including washing one’s hair. He advocated, for example, washing one’s body especially before important ceremonies, which has traditionally been done in India and also in the original Christian tradition.
So this particular effect of a head bath dimming your inner energies and meditations must be a very subjective, personal, psychological or physical issue.
If it is psychological, it may be that some subconscious voice inside you strongly rejects that shower, for some reason, which brings your energy down. If that is the case, affirm to yourself, “This shower is from God and will help my meditations.” In other words, make friends with the head bath.
If instead it is physical, maybe there is a physiological effect which you can change. If you take a relatively cold head bath, try a warm one. Maybe the cold water makes your muscles rigid which blocks the energy. On the contrary, if your head bath is very warm or almost hot, try a cooler one. Very warm water, especially if we absorb it for a longer time, can drain our energies.
May you feel showered by divine Grace,
Jayadev