Under what conditions may an  employer pay his employees’ wages through a bank?

Section 7 of Republic Act No. 6727* provides:

    “Upon written permission of the majority of the employees or workers  concerned, all private establishments, companies, businesses, and  other entities with twenty five (25) or more employees and located  within one (1) kilometer radius to a commercial, savings or rural  bank shall pay the wages and other benefits of their employees  through any of said banks and within the period of payment of wages  fixed by Presidential Decree No. 442, as amended, otherwise known as  the Labor Code of the Philippines.”

*[REPUBLIC ACT NO.  6727]
AN ACT TO RATIONALIZE WAGE POLICY DETERMINATION BY  ESTABLISHING THE MECHANISM AND PROPER STANDARDS THEREFOR, AMENDING FOR  THE PURPOSE ARTICLE 99 OF, AND INCORPORATING ARTICLES 120, 121, 122,  123, 124, 126 AND 127 INTO, PRESIDENTIAL DECREE NO. 442, AS AMENDED,  OTHERWISE KNOWN AS THE LABOR CODE OF THE PHILIPPINES, FIXING NEW WAGE  RATES, PROVIDING WAGE INCENTIVES FOR INDUSTRIAL DISPERSAL TO THE  COUNTRYSIDE, AND FOR OTHER PURPOSES

but it does not preclude companies of less than 25 persons who may opt to pay their employees through a bank does it?

This isnt stated directly based on the quoted article.  So this means it just entirely depends on the verbal agreement between the employees of employers... or mere notification of the employer to its employees.... 

here is a situation.

when a company was at 40 employees, written agreement from 35 of the employees to receive pay through ATMs was created.

however when it reached a population of 400, majority of employees now want to receive pay in cash.

(it is true that this is an improbable situation but for the sake of argument....)

would the company now be obliged to do so? considering that doing so would entail more overhead?

or would the previous agreement still be considered as in effect?

You were right when you said agreement... But mere notification, that's a no no no! Salary is actually the employees money. The employers cannot by any means put that money anywhere they want. Whatever they do, they must ask the consent of the owners first- those are the employees.

Yes, the previous agreement can still be considered in effect. It can be regarded as a company practice.

But what do you think of our situation (in BECI) , overlord?

We were compelled.