El Nido is a very safe place and the island of Palawan is considered to be one of the safest places in the Philippines. There are plenty of opportunities for solo female travellers to make friends on group tours if they wish to have some company.
The biggest safety problem here is the food. Many travellers have reported getting in trouble with food poisoning. It is advised to eat at places where the food turnover is high. It is recommended to avoid sushi and drink lots of water to stay hydrated. Take care of yourself and pack some extra stomach medication in case of illness.
Walking the streets at night is considered OK but exercise caution like any traveller would in any destination and watch your belongings for petty theft.