Scratching your head when your head is feeling itchy is perfectly okay and won't cause any harm.
However scratching your head too often or too hard can damage your scalp so do not scratch your head too hard or too often unless you're feeling itchy.
If your head is constantly itchy then I recommend washing your hair using some Apple Cider Vinegar as Apple Cider Vinegar is antibacterial , anti-inflammatory, and antifungal which means it can kill the bacteria and fungus that could be causing your itchy scalp.
I've had great luck with washing my hair using Apple Cider Vinegar and my hair hasn't been as itchy as a result.
Still it's okay to scratch your head when needed but just don't overdo it to avoid damage to your scalp and hair follicles.