This subject is explained in the Abhidharma thus: There is a kind of force in merit that can be directed or dedicated for a specific purpose, like for example to an increase in one's life span or to healing etc. The fact that generosity, morality, and recitation of sutras posses merit doesn't constitute an outside supernatural being. Dedicating merit for a purpose doesn't constitute a prayer in the theistic sense, far from it.
If we were to debate the validity of supernatural beings in the context of the Nikayas you would find that devas, asuras, nagas, etc. are recognized as valid.
In fact there are records in the Nikayas of devas that personally observe practitioners in the way one in the West might associate with guardian angels. I think it would be difficult to find, but I recall there is a sutta where a monk newly attained arhantship and a deva came to tell the Buddha what had transpired.
Also, suppose someone were to pray to the Buddha who has clairvoyance, or any other benevolent being with clairvoyance and a means to benefit. Why would prayers not be effective when praying so such a being?
The Nikayas acknowledge beings like this, http://www.accesstoinsight.org/tipitaka ... .than.html
"Then the devata inhabiting the forest thicket, feeling sympathy for the monk, desiring his benefit, desiring to bring him to his senses, approached him and addressed him with this verse:
A person ruthless & grasping, smeared like a nursing diaper: to him I have nothing to say. It's you to whom I should speak. To a person unblemished, constantly searching for purity, a hair-tip's worth of evil seems as large as a cloud.
Yes, yakkha, you understand me and show me sympathy. Warn me again, yakkha, whenever again you see something like this. "
I agree, I don't deny the existence of devas, yakshas, brahmas, asuras, etc..., the question is what causes what, i.e. of causation. Buddhism says that existence derives from one's volitions (samskara) that arise because of ignorance (avidya) and so on... (the rest of pratitya samutpada). This is the great difference to the theistic religions. Devas, brahmas, yakshas and asuras arise in the same way (as humans).
Ofcourse one can do something for others, like parents, teachers, friends and relatives can do to children. We do not deny that either. This applies to devas and the rest.
The emphasis is on one's own actions, they are omnipotent. Dhammapada
verse 43: "Neither mother, father, nor any other relative can do one greater good than one's own well directed mind."