While it is true that the Filipino did hide their martial art inside rituals and dances, this has nothing to do with the japanese. The Phillipines were only occupied by Japan for less than 5 years, during World War II.
From what I've gathered, Eskrima is really a catch-all term for a number of Filipino Martial Arts. The stories say that the different styles grew out of the fighting styles of the native tribes of the Phillipines after Spain discovered and invaded them in the 16th Century. Eskrima most probably evolved from those combat techniques that where found to be effective against the invading spaniards and, in at least some styles, spanish fencing. The influence of the spanish can be seen today in many schools of eskrima, and in fact, the word "eskrima" itself comes from the spanish word for fencing.
Disclaimer: I am no expert in the history of Eskrima. In fact, I am not even a practicioner. This w/u was only written to correct the mix-up of the spanish with the japanese in the above w/u.